diff --git a/404.html b/404.html
index 7dbcddd..b493d37 100644
--- a/404.html
+++ b/404.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="https://sydneybiox.github.io/SpatialFeatures/index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/SpatialFeatures.html b/articles/SpatialFeatures.html
index 90bc52a..7747467 100644
--- a/articles/SpatialFeatures.html
+++ b/articles/SpatialFeatures.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -491,7 +491,7 @@ <h2 id="finish">Finish<a class="anchor" aria-label="anchor" href="#finish"></a>
 <span><span class="co">#&gt; [8] methods   base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt;  [1] ggplot2_3.5.1               SpatialFeatures_0.0.5      </span></span>
+<span><span class="co">#&gt;  [1] ggplot2_3.5.1               SpatialFeatures_0.99.0     </span></span>
 <span><span class="co">#&gt;  [3] purrr_1.0.2                 dplyr_1.1.4                </span></span>
 <span><span class="co">#&gt;  [5] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0</span></span>
 <span><span class="co">#&gt;  [7] Biobase_2.64.0              GenomicRanges_1.56.1       </span></span>
diff --git a/articles/index.html b/articles/index.html
index 902c62f..a52c236 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 335bdbc..a11b4a6 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -51,13 +51,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Ghazanfar S (2024).
 <em>SpatialFeatures: Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets</em>.
-R package version 0.0.5, <a href="https://sydneybiox.github.io/SpatialFeatures/">https://sydneybiox.github.io/SpatialFeatures/</a>.
+R package version 0.99.0, <a href="https://sydneybiox.github.io/SpatialFeatures/">https://sydneybiox.github.io/SpatialFeatures/</a>.
 </p>
       <pre>@Manual{,
   title = {SpatialFeatures: Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets},
   author = {Shila Ghazanfar},
   year = {2024},
-  note = {R package version 0.0.5},
+  note = {R package version 0.99.0},
   url = {https://sydneybiox.github.io/SpatialFeatures/},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index d0bdfc4..ab27bbf 100644
--- a/index.html
+++ b/index.html
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index 1f53e1f..315afe8 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@ <h1>Changelog</h1>
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.0.5" id="spatialfeatures-v005-2024-09-19">SpatialFeatures v0.0.5 (2024-09-19)<a class="anchor" aria-label="anchor" href="#spatialfeatures-v005-2024-09-19"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.99.0" id="spatialfeatures-v0990-2024-09-19">SpatialFeatures v0.99.0 (2024-09-19)<a class="anchor" aria-label="anchor" href="#spatialfeatures-v0990-2024-09-19"></a></h2>
 <ul><li>Submitted to Bioconductor.</li>
 </ul></div>
   </main></div>
diff --git a/pkgdown.yml b/pkgdown.yml
index 5a0b801..251acb4 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   SpatialFeatures: SpatialFeatures.html
-last_built: 2024-09-19T01:25Z
+last_built: 2024-09-19T06:37Z
 urls:
   reference: https://sydneybiox.github.io/SpatialFeatures/reference
   article: https://sydneybiox.github.io/SpatialFeatures/articles
diff --git a/reference/CountsMatrix.html b/reference/CountsMatrix.html
index e2cc2b0..7d8beb2 100644
--- a/reference/CountsMatrix.html
+++ b/reference/CountsMatrix.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/EntropyMatrix.html b/reference/EntropyMatrix.html
index 8cfdddd..5ef9c75 100644
--- a/reference/EntropyMatrix.html
+++ b/reference/EntropyMatrix.html
@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/EntropySingleCellExperiment.html b/reference/EntropySingleCellExperiment.html
index e38d70d..599c899 100644
--- a/reference/EntropySingleCellExperiment.html
+++ b/reference/EntropySingleCellExperiment.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/GenerateFeatureData.html b/reference/GenerateFeatureData.html
index 1ba0668..e94a1aa 100644
--- a/reference/GenerateFeatureData.html
+++ b/reference/GenerateFeatureData.html
@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/annuli_counts.html b/reference/annuli_counts.html
index cbecd0b..a74f4af 100644
--- a/reference/annuli_counts.html
+++ b/reference/annuli_counts.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculate_centroids.html b/reference/calculate_centroids.html
index 5e690e8..74369b0 100644
--- a/reference/calculate_centroids.html
+++ b/reference/calculate_centroids.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculate_entropy.html b/reference/calculate_entropy.html
index ae81d48..b5cb18d 100644
--- a/reference/calculate_entropy.html
+++ b/reference/calculate_entropy.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/compute_cell_entropy.html b/reference/compute_cell_entropy.html
index d59eaca..91c3822 100644
--- a/reference/compute_cell_entropy.html
+++ b/reference/compute_cell_entropy.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/countsprop.html b/reference/countsprop.html
index f29d1bc..b81265f 100644
--- a/reference/countsprop.html
+++ b/reference/countsprop.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/create_scaled_df_sub.html b/reference/create_scaled_df_sub.html
index 42cea7e..f9005a1 100644
--- a/reference/create_scaled_df_sub.html
+++ b/reference/create_scaled_df_sub.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/create_scaled_df_super.html b/reference/create_scaled_df_super.html
index c0a2b13..fd3bce6 100644
--- a/reference/create_scaled_df_super.html
+++ b/reference/create_scaled_df_super.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/create_sector_df.html b/reference/create_sector_df.html
index 76a1449..d28f74e 100644
--- a/reference/create_sector_df.html
+++ b/reference/create_sector_df.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/create_sectors.html b/reference/create_sectors.html
index dadd8fb..8e1de62 100644
--- a/reference/create_sectors.html
+++ b/reference/create_sectors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/extract_boundaries.html b/reference/extract_boundaries.html
index dcaa611..34580f7 100644
--- a/reference/extract_boundaries.html
+++ b/reference/extract_boundaries.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/extract_boundaries_and_centroids.html b/reference/extract_boundaries_and_centroids.html
index ed689b5..d428997 100644
--- a/reference/extract_boundaries_and_centroids.html
+++ b/reference/extract_boundaries_and_centroids.html
@@ -7,7 +7,7 @@
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/extract_cell_segments.html b/reference/extract_cell_segments.html
index 794b009..079fcc5 100644
--- a/reference/extract_cell_segments.html
+++ b/reference/extract_cell_segments.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/generate_scale_factors_all.html b/reference/generate_scale_factors_all.html
index 7be4f36..67d4645 100644
--- a/reference/generate_scale_factors_all.html
+++ b/reference/generate_scale_factors_all.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/generate_scale_factors_all_outside.html b/reference/generate_scale_factors_all_outside.html
index 8b1b874..9aa4772 100644
--- a/reference/generate_scale_factors_all_outside.html
+++ b/reference/generate_scale_factors_all_outside.html
@@ -7,7 +7,7 @@
 
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diff --git a/reference/get_cells.html b/reference/get_cells.html
index 14947e6..01be06f 100644
--- a/reference/get_cells.html
+++ b/reference/get_cells.html
@@ -7,7 +7,7 @@
 
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diff --git a/reference/index.html b/reference/index.html
index 2c47775..0739a2a 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
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diff --git a/reference/loadBoundaries.html b/reference/loadBoundaries.html
index 2f6b3c7..ce94637 100644
--- a/reference/loadBoundaries.html
+++ b/reference/loadBoundaries.html
@@ -27,7 +27,7 @@
 
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diff --git a/reference/make_assay_data.html b/reference/make_assay_data.html
index aa5badf..31333a4 100644
--- a/reference/make_assay_data.html
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diff --git a/reference/matrix_entropy.html b/reference/matrix_entropy.html
index 1e5f8e3..191b561 100644
--- a/reference/matrix_entropy.html
+++ b/reference/matrix_entropy.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
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diff --git a/reference/me.html b/reference/me.html
index 40cb942..fcb974c 100644
--- a/reference/me.html
+++ b/reference/me.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/modify_area_id.html b/reference/modify_area_id.html
index eee9670..c4fad9a 100644
--- a/reference/modify_area_id.html
+++ b/reference/modify_area_id.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
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diff --git a/reference/spatialFeatures.html b/reference/spatialFeatures.html
index cb2bde1..7df5325 100644
--- a/reference/spatialFeatures.html
+++ b/reference/spatialFeatures.html
@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">SpatialFeatures</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.5</small>
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diff --git a/search.json b/search.json
index f7077cc..206dcb4 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"spatialfeatures","dir":"Articles","previous_headings":"","what":"SpatialFeatures","title":"An introduction to the SpatialFeatures Package","text":"R package SpatialFeatures contains functions extract features molecule-resolved spatial transcriptomics data using objects MoleculeExperiment class.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"load-required-libraries","dir":"Articles","previous_headings":"SpatialFeatures","what":"Load Required Libraries","title":"An introduction to the SpatialFeatures Package","text":"","code":"library(SpatialFeatures) library(MoleculeExperiment) library(SingleCellExperiment) library(ggplot2) library(dplyr)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"create-example-dataset","dir":"Articles","previous_headings":"SpatialFeatures","what":"Create Example Dataset","title":"An introduction to the SpatialFeatures Package","text":"Load example MoleculeExperiment object Xenium data:","code":"repoDir <- system.file(\"extdata\", package = \"MoleculeExperiment\") repoDir <- paste0(repoDir, \"/xenium_V1_FF_Mouse_Brain\")  me <- readXenium(repoDir, keepCols = \"essential\") me #> MoleculeExperiment class #>  #> molecules slot (1): detected #> - detected: #> samples (2): sample1 sample2 #> -- sample1: #> ---- features (137): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (962) #> ---- location range: [4900,4919.98] x [6400.02,6420] #> -- sample2: #> ---- features (143): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (777) #> ---- location range: [4900.01,4919.98] x [6400.16,6419.97] #>  #>  #> boundaries slot (1): cell #> - cell: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (5): 67500 67512 67515 67521 67527 #> -- sample2: #> ---- segments (9): 65043 65044 ... 65070 65071"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"quick-start","dir":"Articles","previous_headings":"SpatialFeatures","what":"Quick start","title":"An introduction to the SpatialFeatures Package","text":"spatialFeatures function performs three key steps. First, generates new boundaries corresponding feature types. Second, calculates entropy-based metrics feature types. Third, combines information returns SingleCellExperiment object. SpatialFeatures can run following basic command. extract feature types single assay. can also calculate gene counts within spatialFeatures function, either additional concatenated features, feature type belonging assay.","code":"se = spatialFeatures(me) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(4): subsector subconcentric supersector superconcentric #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0): se = spatialFeatures(me, includeCounts = TRUE, concatenateFeatures = FALSE) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(5): subsector subconcentric supersector superconcentric #>   genecount #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0):"},{"path":[]},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"generate-new-boundaries-based-on-subcellular-and-supercellular-features","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Generate new boundaries based on subcellular and supercellular features","title":"An introduction to the SpatialFeatures Package","text":"function loadBoundaries() processes given data () returns feature data based multiple assay types, including: - Sub-Sector - Sub-Concentric - Super-Sector - Super-Concentric","code":"me <- SpatialFeatures::loadBoundaries(me) me #> MoleculeExperiment class #>  #> molecules slot (1): detected #> - detected: #> samples (2): sample1 sample2 #> -- sample1: #> ---- features (137): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (962) #> ---- location range: [4900,4919.98] x [6400.02,6420] #> -- sample2: #> ---- features (143): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (777) #> ---- location range: [4900.01,4919.98] x [6400.16,6419.97] #>  #>  #> boundaries slot (5): cell subsector subconcentric supersector #>   superconcentric #> - cell: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (5): 67500 67512 67515 67521 67527 #> -- sample2: #> ---- segments (9): 65043 65044 ... 65070 65071 #> - subsector: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (60): 67500_01 67500_02 ... 67527_11 67527_12 #> -- sample2: #> ---- segments (108): 65043_01 65043_02 ... 65071_11 65071_12 #> - subconcentric: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (30): 67500_01 67500_02 ... 67527_05 67527_06 #> -- sample2: #> ---- segments (54): 65043_01 65043_02 ... 65071_05 65071_06 #> - supersector: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (55): 67500_01 67500_02 ... 67527_10 67527_11 #> -- sample2: #> ---- segments (99): 65043_01 65043_02 ... 65071_10 65071_11 #> - superconcentric: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (35): 67500_01 67500_02 ... 67527_06 67527_07 #> -- sample2: #> ---- segments (63): 65043_01 65043_02 ... 65071_06 65071_07"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"draw-the-feature-boundary-plots","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Draw the Feature Boundary Plots","title":"An introduction to the SpatialFeatures Package","text":"Visualize spatial molecule cell boundary map SpatialFeature boundaries.","code":"ggplot_me() +   # add molecule points and colour by feature name   geom_point_me(me, byColour = \"feature_id\", size = 0.1) +   # add nuclei segments and colour the border with red   geom_polygon_me(me, assayName = \"subsector\", fill = NA, colour = \"red\") +   # add cell segments and colour by cell id   geom_polygon_me(me, byFill = \"segment_id\", colour = \"black\", alpha = 0.1) +   # zoom in to selected patch area   coord_cartesian(xlim = c(4875, 4950), ylim = c(6385, 6455)) ggplot_me() +   # add molecule points and colour by feature name   geom_point_me(me, byColour = \"feature_id\", size = 0.1) +   # add nuclei segments and colour the border with red   geom_polygon_me(me, assayName = \"subconcentric\", fill = NA, colour = \"red\") +   # add cell segments and colour by cell id   geom_polygon_me(me, byFill = \"segment_id\", colour = \"black\", alpha = 0.1) +   # zoom in to selected patch area   coord_cartesian(xlim = c(4875, 4950), ylim = c(6385, 6455)) ggplot_me() +   # add molecule points and colour by feature name   geom_point_me(me, byColour = \"feature_id\", size = 0.1) +   # add nuclei segments and colour the border with red   geom_polygon_me(me, assayName = \"supersector\", fill = NA, colour = \"blue\") +   # add cell segments and colour by cell id   geom_polygon_me(me, byFill = \"segment_id\", colour = \"black\", alpha = 0.1) +   # zoom in to selected patch area   coord_cartesian(xlim = c(4875, 4950), ylim = c(6385, 6455)) ggplot_me() +   # add molecule points and colour by feature name   geom_point_me(me, byColour = \"feature_id\", size = 0.1) +   # add nuclei segments and colour the border with red   geom_polygon_me(me, assayName = \"superconcentric\", fill = NA, colour = \"blue\") +   # add cell segments and colour by cell id   geom_polygon_me(me, byFill = \"segment_id\", colour = \"black\", alpha = 0.1) +   # zoom in to selected patch area   coord_cartesian(xlim = c(4875, 4950), ylim = c(6385, 6455))"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"create-entropy-matrix","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Create Entropy Matrix","title":"An introduction to the SpatialFeatures Package","text":"function EntropyMatrix() computes entropy counts matrix MoleculeExperiment object based given assay type.","code":"ent = SpatialFeatures::EntropyMatrix(me, c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"), nCores = 1) lapply(ent, head, n = 4) #> $subsector #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     0.5623351     0.6931472     0.6365142     0.6931472 #> Acsbg1            0.6931472     0.6931472     0.6931472     0.0000000 #> Adamts2           0.0000000     0.0000000     0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0             0             0     0.0000000 #> Acsbg1                    0             0             0     0.6931472 #> Adamts2                   0             0             0     0.0000000 #> Adamtsl1                  0             0             0     0.0000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     1.5498260             0     0.6931472             0 #> Acsbg1            0.6931472             0     0.0000000             0 #> Adamts2           0.0000000             0     0.0000000             0 #> Adamtsl1          0.0000000             0     0.0000000             0 #>               sample2.65070 sample2.65071 #> 2010300C02Rik             0     0.0000000 #> Acsbg1                    0     0.6931472 #> Adamts2                   0     0.0000000 #> Adamtsl1                  0     0.0000000 #>  #> $subconcentric #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     0.5623351     0.6931472     0.6365142             0 #> Acsbg1            0.6931472     0.0000000     0.6931472             0 #> Adamts2           0.0000000     0.0000000     0.0000000             0 #> Adamtsl1          0.0000000     0.0000000     0.0000000             0 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0             0             0             0 #> Acsbg1                    0             0             0             0 #> Adamts2                   0             0             0             0 #> Adamtsl1                  0             0             0             0 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     1.2770343             0     0.6931472             0 #> Acsbg1            0.6931472             0     0.0000000             0 #> Adamts2           0.0000000             0     0.0000000             0 #> Adamtsl1          0.0000000             0     0.0000000             0 #>               sample2.65070 sample2.65071 #> 2010300C02Rik             0             0 #> Acsbg1                    0             0 #> Adamts2                   0             0 #> Adamtsl1                  0             0 #>  #> $supersector #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik             0      1.332179     0.6931472     0.6931472 #> Acsbg1                    0      0.000000     0.6931472     0.6931472 #> Adamts2                   0      0.000000     0.0000000     0.0000000 #> Adamtsl1                  0      0.000000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0     0.5623351      1.039721     0.5982696 #> Acsbg1                    0     0.0000000      0.000000     0.9502705 #> Adamts2                   0     0.0000000      0.000000     0.0000000 #> Adamtsl1                  0     0.0000000      0.000000     0.0000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik      0.000000     0.6931472             0     0.0000000 #> Acsbg1             1.559581     1.0114043             0     0.6931472 #> Adamts2            0.000000     0.0000000             0     0.0000000 #> Adamtsl1           0.000000     0.0000000             0     0.0000000 #>               sample2.65070 sample2.65071 #> 2010300C02Rik     0.0000000     0.0000000 #> Acsbg1            0.5623351     0.6365142 #> Adamts2           0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000 #>  #> $superconcentric #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     1.5607104       1.05492     0.6931472     0.0000000 #> Acsbg1            0.6931472       0.00000     0.6931472     0.6931472 #> Adamts2           0.0000000       0.00000     0.0000000     0.0000000 #> Adamtsl1          0.0000000       0.00000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik     0.0000000      1.039721      1.386294      1.549826 #> Acsbg1            0.6931472      0.000000      0.000000      1.054920 #> Adamts2           0.0000000      0.000000      0.000000      0.000000 #> Adamtsl1          0.0000000      0.000000      0.000000      0.000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     0.6931472     0.6931472      1.386294     0.0000000 #> Acsbg1            1.3208883     1.3296613      0.000000     0.6931472 #> Adamts2           0.0000000     0.0000000      0.000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000      0.000000     0.0000000 #>               sample2.65070 sample2.65071 #> 2010300C02Rik     0.6931472     0.0000000 #> Acsbg1            0.6931472     0.6365142 #> Adamts2           0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"create-singlecellexperiment-object","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Create SingleCellExperiment Object","title":"An introduction to the SpatialFeatures Package","text":"function EntropySingleCellExperiment() Convert entropy matrix SingleCellExperiment object. also want gene counts, can include parameter","code":"se = SpatialFeatures::EntropySingleCellExperiment(ent, me) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(4): subsector subconcentric supersector superconcentric #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0): se = EntropySingleCellExperiment(ent, me, includeCounts = TRUE) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(5): subsector subconcentric supersector superconcentric #>   genecount #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0):"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"inspect-the-spatialfeatures-singlecellexperiment-object","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Inspect the SpatialFeatures SingleCellExperiment Object","title":"An introduction to the SpatialFeatures Package","text":"Check structure content SingleCellExperiment object:","code":"se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(5): subsector subconcentric supersector superconcentric #>   genecount #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0): colData(se) #> DataFrame with 14 rows and 5 columns #>                        Cell   Sample_id x_central y_central #>                 <character> <character> <numeric> <numeric> #> sample1.67500 sample1.67500     sample1   4896.19   6415.14 #> sample1.67512 sample1.67512     sample1   4909.74   6411.80 #> sample1.67515 sample1.67515     sample1   4912.42   6402.93 #> sample1.67521 sample1.67521     sample1   4916.01   6415.75 #> sample1.67527 sample1.67527     sample1   4923.68   6414.74 #> ...                     ...         ...       ...       ... #> sample2.65063 sample2.65063     sample2   4928.03   6415.25 #> sample2.65064 sample2.65064     sample2   4896.37   6406.56 #> sample2.65067 sample2.65067     sample2   4923.71   6406.08 #> sample2.65070 sample2.65070     sample2   4902.14   6395.17 #> sample2.65071 sample2.65071     sample2   4920.63   6398.99 #>                                                    boundaries #>                                                        <AsIs> #> sample1.67500 4896.85:6413.46,4895.15:6413.89,4894.30:6417.71 #> sample1.67512 4901.95:6417.07,4901.52:6418.56,4900.89:6419.41 #> sample1.67515 4916.40:6412.61,4912.15:6420.05,4910.45:6430.89 #> sample1.67521 4911.51:6397.95,4907.48:6400.71,4904.07:6407.30 #> sample1.67527 4929.57:6408.36,4924.69:6409.85,4921.29:6409.85 #> ...                                                       ... #> sample2.65063 4904.71:6399.65,4898.76:6401.35,4894.30:6407.94 #> sample2.65064 4905.77:6404.11,4906.20:6407.73,4907.05:6412.19 #> sample2.65067 4908.96:6395.61,4904.93:6399.44,4905.56:6403.26 #> sample2.65070 4919.59:6408.36,4915.98:6411.34,4915.76:6411.98 #> sample2.65071 4922.35:6404.54,4919.80:6407.94,4920.23:6413.46 rowData(se) #> DataFrame with 178 rows and 0 columns"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"finish","dir":"Articles","previous_headings":"","what":"Finish","title":"An introduction to the SpatialFeatures Package","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.5 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] parallel  stats4    stats     graphics  grDevices utils     datasets  #> [8] methods   base      #>  #> other attached packages: #>  [1] ggplot2_3.5.1               SpatialFeatures_0.0.5       #>  [3] purrr_1.0.2                 dplyr_1.1.4                 #>  [5] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 #>  [7] Biobase_2.64.0              GenomicRanges_1.56.1        #>  [9] GenomeInfoDb_1.40.1         IRanges_2.38.1              #> [11] S4Vectors_0.42.1            BiocGenerics_0.50.0         #> [13] MatrixGenerics_1.16.0       matrixStats_1.4.1           #> [15] MoleculeExperiment_1.4.1    BiocStyle_2.32.1            #>  #> loaded via a namespace (and not attached): #>  [1] tidyselect_1.2.1         EBImage_4.46.0           farver_2.1.2             #>  [4] bitops_1.0-8             fastmap_1.2.0            RCurl_1.98-1.16          #>  [7] digest_0.6.37            lifecycle_1.0.4          terra_1.7-78             #> [10] magrittr_2.0.3           compiler_4.4.1           rlang_1.1.4              #> [13] sass_0.4.9               tools_4.4.1              utf8_1.2.4               #> [16] yaml_2.3.10              data.table_1.16.0        knitr_1.48               #> [19] labeling_0.4.3           S4Arrays_1.4.1           htmlwidgets_1.6.4        #> [22] bit_4.0.5                DelayedArray_0.30.1      abind_1.4-8              #> [25] BiocParallel_1.38.0      withr_3.0.1              desc_1.4.3               #> [28] grid_4.4.1               fansi_1.0.6              colorspace_2.1-1         #> [31] scales_1.3.0             cli_3.6.3                rmarkdown_2.28           #> [34] crayon_1.5.3             ragg_1.3.3               generics_0.1.3           #> [37] httr_1.4.7               rjson_0.2.23             cachem_1.1.0             #> [40] zlibbioc_1.50.0          BiocManager_1.30.25      XVector_0.44.0           #> [43] tiff_0.1-12              vctrs_0.6.5              Matrix_1.7-0             #> [46] jsonlite_1.8.8           bookdown_0.40            fftwtools_0.9-11         #> [49] bit64_4.0.5              systemfonts_1.1.0        jpeg_0.1-10              #> [52] magick_2.8.4             locfit_1.5-9.10          jquerylib_0.1.4          #> [55] glue_1.7.0               pkgdown_2.1.1            codetools_0.2-20         #> [58] gtable_0.3.5             UCSC.utils_1.0.0         munsell_0.5.1            #> [61] tibble_3.2.1             pillar_1.9.0             htmltools_0.5.8.1        #> [64] GenomeInfoDbData_1.2.12  R6_2.5.1                 textshaping_0.4.0        #> [67] evaluate_1.0.0           lattice_0.22-6           highr_0.11               #> [70] png_0.1-8                SpatialExperiment_1.14.0 bslib_0.8.0              #> [73] Rcpp_1.0.13              SparseArray_1.4.8        xfun_0.47                #> [76] fs_1.6.4                 pkgconfig_2.0.3"},{"path":"https://sydneybiox.github.io/SpatialFeatures/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Shila Ghazanfar. Author, maintainer, contributor. Guan Gui. Contributor.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ghazanfar S (2024). SpatialFeatures: Entropy-based subcellular supercellular features molecule-resolved spatial omics datasets. R package version 0.0.5, https://sydneybiox.github.io/SpatialFeatures/.","code":"@Manual{,   title = {SpatialFeatures: Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets},   author = {Shila Ghazanfar},   year = {2024},   note = {R package version 0.0.5},   url = {https://sydneybiox.github.io/SpatialFeatures/}, }"},{"path":"https://sydneybiox.github.io/SpatialFeatures/index.html","id":"spatialfeatures","dir":"","previous_headings":"","what":"Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets","title":"Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets","text":"R package incorprate features molecule-resolved spatial transcriptomics data. usage instructions package can found vignettes folder.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets","text":"can install SpatialFeatures GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"SydneyBioX/SpatialFeatures\")"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"function retrieves counts matrix Molecule Experiment object based given assay type.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"","code":"CountsMatrix(me, assayName, nCores = 1, ...)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"Molecule Experiment object. assayName character string indicating assay type. Supported values include \"sub-sector\", \"sub-concentric\", \"sub-combo\", \"super-concentric\", \"super-combo\". nCores Number cores parallel processing (default 1) ... arguments passing MoleculeExperiment::countMolecules","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"counts matrix corresponding specified assay type.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"","code":"# Assuming `data_obj` is your Molecule Experiment object # cm = CountsMatrix(data_obj, assayName = \"sub-sector\")"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"function computes entropy counts matrix MoleculeExperiment object based given assay type.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"","code":"EntropyMatrix(me, featureTypes, nCores = 1, ...)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"Molecule Experiment object. featureTypes character string specifying feature type. Supported values include \"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\". nCores Number cores ... arguments passing CountsMatrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"matrix representing entropy values corresponding given assay type.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"","code":"data(example_me) me <- loadBoundaries(me) ent <- EntropyMatrix(me, c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"), nCores = 1) lapply(ent, head, n = 4) #> $subsector #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     0.5623351     0.6931472     0.6365142     0.6931472 #> Acsbg1            0.6931472     0.6931472     0.6931472     0.0000000 #> Adamts2           0.0000000     0.0000000     0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0             0             0     0.0000000 #> Acsbg1                    0             0             0     0.6931472 #> Adamts2                   0             0             0     0.0000000 #> Adamtsl1                  0             0             0     0.0000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     1.5498260             0     0.6931472             0 #> Acsbg1            0.6931472             0     0.0000000             0 #> Adamts2           0.0000000             0     0.0000000             0 #> Adamtsl1          0.0000000             0     0.0000000             0 #>               sample2.65070 sample2.65071 #> 2010300C02Rik             0     0.0000000 #> Acsbg1                    0     0.6931472 #> Adamts2                   0     0.0000000 #> Adamtsl1                  0     0.0000000 #>  #> $subconcentric #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     0.5623351     0.6931472     0.6365142             0 #> Acsbg1            0.6931472     0.0000000     0.6931472             0 #> Adamts2           0.0000000     0.0000000     0.0000000             0 #> Adamtsl1          0.0000000     0.0000000     0.0000000             0 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0             0             0             0 #> Acsbg1                    0             0             0             0 #> Adamts2                   0             0             0             0 #> Adamtsl1                  0             0             0             0 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     1.2770343             0     0.6931472             0 #> Acsbg1            0.6931472             0     0.0000000             0 #> Adamts2           0.0000000             0     0.0000000             0 #> Adamtsl1          0.0000000             0     0.0000000             0 #>               sample2.65070 sample2.65071 #> 2010300C02Rik             0             0 #> Acsbg1                    0             0 #> Adamts2                   0             0 #> Adamtsl1                  0             0 #>  #> $supersector #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik             0      1.332179     0.6931472     0.6931472 #> Acsbg1                    0      0.000000     0.6931472     0.6931472 #> Adamts2                   0      0.000000     0.0000000     0.0000000 #> Adamtsl1                  0      0.000000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0     0.5623351      1.039721     0.5982696 #> Acsbg1                    0     0.0000000      0.000000     0.9502705 #> Adamts2                   0     0.0000000      0.000000     0.0000000 #> Adamtsl1                  0     0.0000000      0.000000     0.0000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik      0.000000     0.6931472             0     0.0000000 #> Acsbg1             1.559581     1.0114043             0     0.6931472 #> Adamts2            0.000000     0.0000000             0     0.0000000 #> Adamtsl1           0.000000     0.0000000             0     0.0000000 #>               sample2.65070 sample2.65071 #> 2010300C02Rik     0.0000000     0.0000000 #> Acsbg1            0.5623351     0.6365142 #> Adamts2           0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000 #>  #> $superconcentric #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     1.5607104       1.05492     0.6931472     0.0000000 #> Acsbg1            0.6931472       0.00000     0.6931472     0.6931472 #> Adamts2           0.0000000       0.00000     0.0000000     0.0000000 #> Adamtsl1          0.0000000       0.00000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik     0.0000000      1.039721      1.386294      1.549826 #> Acsbg1            0.6931472      0.000000      0.000000      1.054920 #> Adamts2           0.0000000      0.000000      0.000000      0.000000 #> Adamtsl1          0.0000000      0.000000      0.000000      0.000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     0.6931472     0.6931472      1.386294     0.0000000 #> Acsbg1            1.3208883     1.3296613      0.000000     0.6931472 #> Adamts2           0.0000000     0.0000000      0.000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000      0.000000     0.0000000 #>               sample2.65070 sample2.65071 #> 2010300C02Rik     0.6931472     0.0000000 #> Acsbg1            0.6931472     0.6365142 #> Adamts2           0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000 #>"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"function takes list data frames Molecule Experiment object constructs SingleCellExperiment object specified data structure.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"","code":"EntropySingleCellExperiment(   df_list,   me,   includeCounts = FALSE,   concatenateFeatures = FALSE,   nCores = 1 )"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"df_list list data frames, containing assay data. Molecule Experiment object. includeCounts logical (default FALSE) whether include gene counts features concatenateFeatures logical whether concatenate features single assay (default FALSE). FALSE output SE object multiple assays nCores Number cores (default 1)","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"SingleCellExperiment object.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"","code":"data(example_me) me <- loadBoundaries(me) ent <- EntropyMatrix(me, c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"), nCores = 1) se <- EntropySingleCellExperiment(ent, me) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(4): subsector subconcentric supersector superconcentric #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0):"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/GenerateFeatureData.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","title":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","text":"comprehensive function processes given data () returns feature data based multiple assay types. supported assays encapsulated within function include: Sub-sector polygons Sub-concentric polygons Sub-combo polygons Super-concentric polygons Super-combo polygons assays represent various spatial subdivisions transformations, addressing unique feature characteristics. results assay combined returned list dataframes.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/GenerateFeatureData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","text":"","code":"GenerateFeatureData(   me,   featureTypes = c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"),   k = 5 )"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/GenerateFeatureData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","text":"input data object. object contains spatial information, typically regarding segments regions interest. featureTypes Character vector containing feature types calculate. k numeric value indicating scaling factor concentric polygons. Defaults 5.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/GenerateFeatureData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","text":"list containing dataframes assay type: subsector: Feature data sub-sector polygons. subconcentric: Feature data sub-concentric polygons. supersector: Feature data super-sector polygons. superconcentric: Feature data super-concentric polygons.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/annuli_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","title":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","text":"Convert cumulative counts concentric polygons annuli polygon counts","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/annuli_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","text":"","code":"annuli_counts(mat)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/annuli_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","text":"mat matrix cumulative counts.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/annuli_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","text":"matrix annuli polygon counts.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_centroids.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate centroids from boundaries — calculate_centroids","title":"Calculate centroids from boundaries — calculate_centroids","text":"Calculate centroids boundaries","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_centroids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate centroids from boundaries — calculate_centroids","text":"","code":"calculate_centroids(df_boundary)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_centroids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate centroids from boundaries — calculate_centroids","text":"df_boundary data frame boundaries.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_centroids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate centroids from boundaries — calculate_centroids","text":"data frame centroids.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_entropy.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate entropy from a probability vector — calculate_entropy","title":"Calculate entropy from a probability vector — calculate_entropy","text":"Calculate entropy probability vector","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_entropy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate entropy from a probability vector — calculate_entropy","text":"","code":"calculate_entropy(p)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_entropy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate entropy from a probability vector — calculate_entropy","text":"p numeric vector probabilities.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_entropy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate entropy from a probability vector — calculate_entropy","text":"calculated entropy value.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/compute_cell_entropy.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute entropy for a given matrix — compute_cell_entropy","title":"Compute entropy for a given matrix — compute_cell_entropy","text":"Compute entropy given matrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/compute_cell_entropy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute entropy for a given matrix — compute_cell_entropy","text":"","code":"compute_cell_entropy(cell_segments_mat)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/compute_cell_entropy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute entropy for a given matrix — compute_cell_entropy","text":"cell_segments_mat matrix compute entropy .","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/compute_cell_entropy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute entropy for a given matrix — compute_cell_entropy","text":"vector entropy values.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/countsprop.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate prop for entropy — countsprop","title":"Calculate prop for entropy — countsprop","text":"Calculate prop entropy","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/countsprop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate prop for entropy — countsprop","text":"","code":"countsprop(counts)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/countsprop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate prop for entropy — countsprop","text":"counts vector integers","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/countsprop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate prop for entropy — countsprop","text":"proportion","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_sub.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a scaled data frame — create_scaled_df_sub","title":"Create a scaled data frame — create_scaled_df_sub","text":"Create scaled data frame","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_sub.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a scaled data frame — create_scaled_df_sub","text":"","code":"create_scaled_df_sub(s, df_circle, k = 5)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_sub.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a scaled data frame — create_scaled_df_sub","text":"s numeric scaling factor. df_circle data frame scale. k numeric value, defaulting 8.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_sub.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a scaled data frame — create_scaled_df_sub","text":"scaled data frame.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_super.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a scaled data frame — create_scaled_df_super","title":"Create a scaled data frame — create_scaled_df_super","text":"Create scaled data frame","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_super.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a scaled data frame — create_scaled_df_super","text":"","code":"create_scaled_df_super(s, df_circle, k = 5)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_super.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a scaled data frame — create_scaled_df_super","text":"s numeric scaling factor. df_circle data frame scale. k numeric value, defaulting 8.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_super.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a scaled data frame — create_scaled_df_super","text":"scaled data frame.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sector_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Create sector data frame from circle data — create_sector_df","title":"Create sector data frame from circle data — create_sector_df","text":"function takes data frame circle data segment IDs locations, returns data frame sectors scaled coordinates.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sector_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create sector data frame from circle data — create_sector_df","text":"","code":"create_sector_df(df)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sector_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create sector data frame from circle data — create_sector_df","text":"df data frame containing circle data segment IDs, x y locations.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sector_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create sector data frame from circle data — create_sector_df","text":"data frame coordinates sector.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Create sectors from a given data frame — create_sectors","title":"Create sectors from a given data frame — create_sectors","text":"Create sectors given data frame","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create sectors from a given data frame — create_sectors","text":"","code":"create_sectors(df)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create sectors from a given data frame — create_sectors","text":"df data frame create sectors .","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create sectors from a given data frame — create_sectors","text":"data frame sectors.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract boundaries from a given object — extract_boundaries","title":"Extract boundaries from a given object — extract_boundaries","text":"Extract boundaries given object","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract boundaries from a given object — extract_boundaries","text":"","code":"extract_boundaries(me)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract boundaries from a given object — extract_boundaries","text":"object extract boundaries .","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract boundaries from a given object — extract_boundaries","text":"data frame extracted boundaries.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries_and_centroids.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","title":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","text":"Extract boundaries calculate centroids","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries_and_centroids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","text":"","code":"extract_boundaries_and_centroids(me)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries_and_centroids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","text":"object process.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries_and_centroids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","text":"list containing data frame boundaries data frame centroids.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_cell_segments.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","title":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","text":"Extract submatrix corresponding segment matrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_cell_segments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","text":"","code":"extract_cell_segments(mat, cell)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_cell_segments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","text":"mat matrix process. cell character string indicating segment extract.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_cell_segments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","text":"submatrix provided matrix.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate scale factors for all values of k — generate_scale_factors_all","title":"Generate scale factors for all values of k — generate_scale_factors_all","text":"Generate scale factors values k","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate scale factors for all values of k — generate_scale_factors_all","text":"","code":"generate_scale_factors_all(k)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate scale factors for all values of k — generate_scale_factors_all","text":"k numeric value.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate scale factors for all values of k — generate_scale_factors_all","text":"vector scale factors.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all_outside.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","title":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","text":"Generate scale factors outside values ks","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all_outside.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","text":"","code":"generate_scale_factors_all_outside(k)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all_outside.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","text":"k numeric value.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all_outside.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","text":"vector scale factors outside values.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/get_cells.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract unique segments from matrix column names — get_cells","title":"Extract unique segments from matrix column names — get_cells","text":"Extract unique segments matrix column names","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/get_cells.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract unique segments from matrix column names — get_cells","text":"","code":"get_cells(mat)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/get_cells.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract unique segments from matrix column names — get_cells","text":"mat matrix process.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/get_cells.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract unique segments from matrix column names — get_cells","text":"character vector unique segments.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":null,"dir":"Reference","previous_headings":"","what":"Load Boundaries to Molecule Experiment Object — loadBoundaries","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"function takes Molecule Experiment () object input enriches boundary data variety assays. currently supported assays : Sub-sector polygons Sub-concentric polygons Super-sector polygons Super-concentric polygons function internally processes assay, extracts respective boundary information, updates original object new data.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"","code":"loadBoundaries(me, ...)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"MoleculeExperiment () object ... arguments passed GenerateFeatureData","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"enriched Molecule Experiment () object includes boundary information supported assays.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"","code":"data(example_me) me <- loadBoundaries(me) me #> MoleculeExperiment class #>  #> molecules slot (1): detected #> - detected: #> samples (2): sample1 sample2 #> -- sample1: #> ---- features (137): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (962) #> ---- location range: [4900,4919.98] x [6400.02,6420] #> -- sample2: #> ---- features (143): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (777) #> ---- location range: [4900.01,4919.98] x [6400.16,6419.97] #>  #>  #> boundaries slot (5): cell subsector subconcentric supersector #>   superconcentric #> - cell: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (5): 67500 67512 67515 67521 67527 #> -- sample2: #> ---- segments (9): 65043 65044 ... 65070 65071 #> - subsector: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (60): 67500_01 67500_02 ... 67527_11 67527_12 #> -- sample2: #> ---- segments (108): 65043_01 65043_02 ... 65071_11 65071_12 #> - subconcentric: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (30): 67500_01 67500_02 ... 67527_05 67527_06 #> -- sample2: #> ---- segments (54): 65043_01 65043_02 ... 65071_05 65071_06 #> - supersector: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (55): 67500_01 67500_02 ... 67527_10 67527_11 #> -- sample2: #> ---- segments (99): 65043_01 65043_02 ... 65071_10 65071_11 #> - superconcentric: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (35): 67500_01 67500_02 ... 67527_06 67527_07 #> -- sample2: #> ---- segments (63): 65043_01 65043_02 ... 65071_06 65071_07"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/make_assay_data.html","id":null,"dir":"Reference","previous_headings":"","what":"make assay data — make_assay_data","title":"make assay data — make_assay_data","text":"make assay data","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/make_assay_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"make assay data — make_assay_data","text":"","code":"make_assay_data(df_list, concatenateFeatures = FALSE)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/make_assay_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"make assay data — make_assay_data","text":"df_list list data frames concatenateFeatures logical whether concatenate features (default FALSE)","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/make_assay_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"make assay data — make_assay_data","text":"concatenateFeatures == TRUE, single data frame, otherwise list containing data frames","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/matrix_entropy.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute entropy for the entire matrix — matrix_entropy","title":"Compute entropy for the entire matrix — matrix_entropy","text":"Compute entropy entire matrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/matrix_entropy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute entropy for the entire matrix — matrix_entropy","text":"","code":"matrix_entropy(mat, nCores = 1)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/matrix_entropy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute entropy for the entire matrix — matrix_entropy","text":"mat matrix compute entropy . nCores Number cores","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/matrix_entropy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute entropy for the entire matrix — matrix_entropy","text":"data frame entropy values matrix.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/me.html","id":null,"dir":"Reference","previous_headings":"","what":"Example MoleculeExperiment data — me","title":"Example MoleculeExperiment data — me","text":"tiny object containing cells molecules","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/me.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example MoleculeExperiment data — me","text":"","code":"data(example_me, package = 'SpatialFeatures')"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/me.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example MoleculeExperiment data — me","text":"MoleculeExperiment object.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/modify_area_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify the area_id format — modify_area_id","title":"Modify the area_id format — modify_area_id","text":"function takes area_id string modifies last segment single-digit number 1 9 adding leading zero.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/modify_area_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify the area_id format — modify_area_id","text":"","code":"modify_area_id(id)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/modify_area_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify the area_id format — modify_area_id","text":"id string representing area_id.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/modify_area_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify the area_id format — modify_area_id","text":"string modified area_id format.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate SpatialFeatures — spatialFeatures","title":"Calculate SpatialFeatures — spatialFeatures","text":"function takes MoleculeExperiment () object input calculates new molecule-based spatial features according following segmentations: Sub-sector polygons Sub-concentric polygons Super-sector polygons Super-concentric polygons function 3 key steps, 1. adds new boundaries object according subcellular supercellular segmentations, 2. calculates entropy cell featureType combinations, 3. combines entropy values SingleCellExperiment object.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate SpatialFeatures — spatialFeatures","text":"","code":"spatialFeatures(   me,   featureTypes = c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"),   k = 5,   nCores = 1,   includeCounts = FALSE,   concatenateFeatures = FALSE,   ... )"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate SpatialFeatures — spatialFeatures","text":"MoleculeExperiment () object featureTypes character string specifying feature type. Supported values include \"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\". k numeric value indicating number polygons calculate entropy (default 5) nCores number cores parallel processing (default 1) includeCounts logical (default FALSE) whether include gene counts features concatenateFeatures logical whether concatenate features single assay (default FALSE). FALSE output SE object multiple assays ... arguments passed loadBoundaries EntropyMatrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate SpatialFeatures — spatialFeatures","text":"SingleCellExperiment object containing spatialFeatures assay cell-level colData","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate SpatialFeatures — spatialFeatures","text":"","code":"data(example_me) se <- spatialFeatures(me) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(4): subsector subconcentric supersector superconcentric #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0):"},{"path":"https://sydneybiox.github.io/SpatialFeatures/news/index.html","id":"spatialfeatures-v005-2024-09-19","dir":"Changelog","previous_headings":"","what":"SpatialFeatures v0.0.5 (2024-09-19)","title":"SpatialFeatures v0.0.5 (2024-09-19)","text":"Submitted Bioconductor.","code":""}]
+[{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"spatialfeatures","dir":"Articles","previous_headings":"","what":"SpatialFeatures","title":"An introduction to the SpatialFeatures Package","text":"R package SpatialFeatures contains functions extract features molecule-resolved spatial transcriptomics data using objects MoleculeExperiment class.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"load-required-libraries","dir":"Articles","previous_headings":"SpatialFeatures","what":"Load Required Libraries","title":"An introduction to the SpatialFeatures Package","text":"","code":"library(SpatialFeatures) library(MoleculeExperiment) library(SingleCellExperiment) library(ggplot2) library(dplyr)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"create-example-dataset","dir":"Articles","previous_headings":"SpatialFeatures","what":"Create Example Dataset","title":"An introduction to the SpatialFeatures Package","text":"Load example MoleculeExperiment object Xenium data:","code":"repoDir <- system.file(\"extdata\", package = \"MoleculeExperiment\") repoDir <- paste0(repoDir, \"/xenium_V1_FF_Mouse_Brain\")  me <- readXenium(repoDir, keepCols = \"essential\") me #> MoleculeExperiment class #>  #> molecules slot (1): detected #> - detected: #> samples (2): sample1 sample2 #> -- sample1: #> ---- features (137): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (962) #> ---- location range: [4900,4919.98] x [6400.02,6420] #> -- sample2: #> ---- features (143): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (777) #> ---- location range: [4900.01,4919.98] x [6400.16,6419.97] #>  #>  #> boundaries slot (1): cell #> - cell: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (5): 67500 67512 67515 67521 67527 #> -- sample2: #> ---- segments (9): 65043 65044 ... 65070 65071"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"quick-start","dir":"Articles","previous_headings":"SpatialFeatures","what":"Quick start","title":"An introduction to the SpatialFeatures Package","text":"spatialFeatures function performs three key steps. First, generates new boundaries corresponding feature types. Second, calculates entropy-based metrics feature types. Third, combines information returns SingleCellExperiment object. SpatialFeatures can run following basic command. extract feature types single assay. can also calculate gene counts within spatialFeatures function, either additional concatenated features, feature type belonging assay.","code":"se = spatialFeatures(me) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(4): subsector subconcentric supersector superconcentric #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0): se = spatialFeatures(me, includeCounts = TRUE, concatenateFeatures = FALSE) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(5): subsector subconcentric supersector superconcentric #>   genecount #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0):"},{"path":[]},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"generate-new-boundaries-based-on-subcellular-and-supercellular-features","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Generate new boundaries based on subcellular and supercellular features","title":"An introduction to the SpatialFeatures Package","text":"function loadBoundaries() processes given data () returns feature data based multiple assay types, including: - Sub-Sector - Sub-Concentric - Super-Sector - Super-Concentric","code":"me <- SpatialFeatures::loadBoundaries(me) me #> MoleculeExperiment class #>  #> molecules slot (1): detected #> - detected: #> samples (2): sample1 sample2 #> -- sample1: #> ---- features (137): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (962) #> ---- location range: [4900,4919.98] x [6400.02,6420] #> -- sample2: #> ---- features (143): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (777) #> ---- location range: [4900.01,4919.98] x [6400.16,6419.97] #>  #>  #> boundaries slot (5): cell subsector subconcentric supersector #>   superconcentric #> - cell: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (5): 67500 67512 67515 67521 67527 #> -- sample2: #> ---- segments (9): 65043 65044 ... 65070 65071 #> - subsector: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (60): 67500_01 67500_02 ... 67527_11 67527_12 #> -- sample2: #> ---- segments (108): 65043_01 65043_02 ... 65071_11 65071_12 #> - subconcentric: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (30): 67500_01 67500_02 ... 67527_05 67527_06 #> -- sample2: #> ---- segments (54): 65043_01 65043_02 ... 65071_05 65071_06 #> - supersector: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (55): 67500_01 67500_02 ... 67527_10 67527_11 #> -- sample2: #> ---- segments (99): 65043_01 65043_02 ... 65071_10 65071_11 #> - superconcentric: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (35): 67500_01 67500_02 ... 67527_06 67527_07 #> -- sample2: #> ---- segments (63): 65043_01 65043_02 ... 65071_06 65071_07"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"draw-the-feature-boundary-plots","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Draw the Feature Boundary Plots","title":"An introduction to the SpatialFeatures Package","text":"Visualize spatial molecule cell boundary map SpatialFeature boundaries.","code":"ggplot_me() +   # add molecule points and colour by feature name   geom_point_me(me, byColour = \"feature_id\", size = 0.1) +   # add nuclei segments and colour the border with red   geom_polygon_me(me, assayName = \"subsector\", fill = NA, colour = \"red\") +   # add cell segments and colour by cell id   geom_polygon_me(me, byFill = \"segment_id\", colour = \"black\", alpha = 0.1) +   # zoom in to selected patch area   coord_cartesian(xlim = c(4875, 4950), ylim = c(6385, 6455)) ggplot_me() +   # add molecule points and colour by feature name   geom_point_me(me, byColour = \"feature_id\", size = 0.1) +   # add nuclei segments and colour the border with red   geom_polygon_me(me, assayName = \"subconcentric\", fill = NA, colour = \"red\") +   # add cell segments and colour by cell id   geom_polygon_me(me, byFill = \"segment_id\", colour = \"black\", alpha = 0.1) +   # zoom in to selected patch area   coord_cartesian(xlim = c(4875, 4950), ylim = c(6385, 6455)) ggplot_me() +   # add molecule points and colour by feature name   geom_point_me(me, byColour = \"feature_id\", size = 0.1) +   # add nuclei segments and colour the border with red   geom_polygon_me(me, assayName = \"supersector\", fill = NA, colour = \"blue\") +   # add cell segments and colour by cell id   geom_polygon_me(me, byFill = \"segment_id\", colour = \"black\", alpha = 0.1) +   # zoom in to selected patch area   coord_cartesian(xlim = c(4875, 4950), ylim = c(6385, 6455)) ggplot_me() +   # add molecule points and colour by feature name   geom_point_me(me, byColour = \"feature_id\", size = 0.1) +   # add nuclei segments and colour the border with red   geom_polygon_me(me, assayName = \"superconcentric\", fill = NA, colour = \"blue\") +   # add cell segments and colour by cell id   geom_polygon_me(me, byFill = \"segment_id\", colour = \"black\", alpha = 0.1) +   # zoom in to selected patch area   coord_cartesian(xlim = c(4875, 4950), ylim = c(6385, 6455))"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"create-entropy-matrix","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Create Entropy Matrix","title":"An introduction to the SpatialFeatures Package","text":"function EntropyMatrix() computes entropy counts matrix MoleculeExperiment object based given assay type.","code":"ent = SpatialFeatures::EntropyMatrix(me, c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"), nCores = 1) lapply(ent, head, n = 4) #> $subsector #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     0.5623351     0.6931472     0.6365142     0.6931472 #> Acsbg1            0.6931472     0.6931472     0.6931472     0.0000000 #> Adamts2           0.0000000     0.0000000     0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0             0             0     0.0000000 #> Acsbg1                    0             0             0     0.6931472 #> Adamts2                   0             0             0     0.0000000 #> Adamtsl1                  0             0             0     0.0000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     1.5498260             0     0.6931472             0 #> Acsbg1            0.6931472             0     0.0000000             0 #> Adamts2           0.0000000             0     0.0000000             0 #> Adamtsl1          0.0000000             0     0.0000000             0 #>               sample2.65070 sample2.65071 #> 2010300C02Rik             0     0.0000000 #> Acsbg1                    0     0.6931472 #> Adamts2                   0     0.0000000 #> Adamtsl1                  0     0.0000000 #>  #> $subconcentric #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     0.5623351     0.6931472     0.6365142             0 #> Acsbg1            0.6931472     0.0000000     0.6931472             0 #> Adamts2           0.0000000     0.0000000     0.0000000             0 #> Adamtsl1          0.0000000     0.0000000     0.0000000             0 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0             0             0             0 #> Acsbg1                    0             0             0             0 #> Adamts2                   0             0             0             0 #> Adamtsl1                  0             0             0             0 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     1.2770343             0     0.6931472             0 #> Acsbg1            0.6931472             0     0.0000000             0 #> Adamts2           0.0000000             0     0.0000000             0 #> Adamtsl1          0.0000000             0     0.0000000             0 #>               sample2.65070 sample2.65071 #> 2010300C02Rik             0             0 #> Acsbg1                    0             0 #> Adamts2                   0             0 #> Adamtsl1                  0             0 #>  #> $supersector #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik             0      1.332179     0.6931472     0.6931472 #> Acsbg1                    0      0.000000     0.6931472     0.6931472 #> Adamts2                   0      0.000000     0.0000000     0.0000000 #> Adamtsl1                  0      0.000000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0     0.5623351      1.039721     0.5982696 #> Acsbg1                    0     0.0000000      0.000000     0.9502705 #> Adamts2                   0     0.0000000      0.000000     0.0000000 #> Adamtsl1                  0     0.0000000      0.000000     0.0000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik      0.000000     0.6931472             0     0.0000000 #> Acsbg1             1.559581     1.0114043             0     0.6931472 #> Adamts2            0.000000     0.0000000             0     0.0000000 #> Adamtsl1           0.000000     0.0000000             0     0.0000000 #>               sample2.65070 sample2.65071 #> 2010300C02Rik     0.0000000     0.0000000 #> Acsbg1            0.5623351     0.6365142 #> Adamts2           0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000 #>  #> $superconcentric #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     1.5607104       1.05492     0.6931472     0.0000000 #> Acsbg1            0.6931472       0.00000     0.6931472     0.6931472 #> Adamts2           0.0000000       0.00000     0.0000000     0.0000000 #> Adamtsl1          0.0000000       0.00000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik     0.0000000      1.039721      1.386294      1.549826 #> Acsbg1            0.6931472      0.000000      0.000000      1.054920 #> Adamts2           0.0000000      0.000000      0.000000      0.000000 #> Adamtsl1          0.0000000      0.000000      0.000000      0.000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     0.6931472     0.6931472      1.386294     0.0000000 #> Acsbg1            1.3208883     1.3296613      0.000000     0.6931472 #> Adamts2           0.0000000     0.0000000      0.000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000      0.000000     0.0000000 #>               sample2.65070 sample2.65071 #> 2010300C02Rik     0.6931472     0.0000000 #> Acsbg1            0.6931472     0.6365142 #> Adamts2           0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"create-singlecellexperiment-object","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Create SingleCellExperiment Object","title":"An introduction to the SpatialFeatures Package","text":"function EntropySingleCellExperiment() Convert entropy matrix SingleCellExperiment object. also want gene counts, can include parameter","code":"se = SpatialFeatures::EntropySingleCellExperiment(ent, me) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(4): subsector subconcentric supersector superconcentric #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0): se = EntropySingleCellExperiment(ent, me, includeCounts = TRUE) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(5): subsector subconcentric supersector superconcentric #>   genecount #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0):"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"inspect-the-spatialfeatures-singlecellexperiment-object","dir":"Articles","previous_headings":"Step-by-step SpatialFeatures","what":"Inspect the SpatialFeatures SingleCellExperiment Object","title":"An introduction to the SpatialFeatures Package","text":"Check structure content SingleCellExperiment object:","code":"se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(5): subsector subconcentric supersector superconcentric #>   genecount #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0): colData(se) #> DataFrame with 14 rows and 5 columns #>                        Cell   Sample_id x_central y_central #>                 <character> <character> <numeric> <numeric> #> sample1.67500 sample1.67500     sample1   4896.19   6415.14 #> sample1.67512 sample1.67512     sample1   4909.74   6411.80 #> sample1.67515 sample1.67515     sample1   4912.42   6402.93 #> sample1.67521 sample1.67521     sample1   4916.01   6415.75 #> sample1.67527 sample1.67527     sample1   4923.68   6414.74 #> ...                     ...         ...       ...       ... #> sample2.65063 sample2.65063     sample2   4928.03   6415.25 #> sample2.65064 sample2.65064     sample2   4896.37   6406.56 #> sample2.65067 sample2.65067     sample2   4923.71   6406.08 #> sample2.65070 sample2.65070     sample2   4902.14   6395.17 #> sample2.65071 sample2.65071     sample2   4920.63   6398.99 #>                                                    boundaries #>                                                        <AsIs> #> sample1.67500 4896.85:6413.46,4895.15:6413.89,4894.30:6417.71 #> sample1.67512 4901.95:6417.07,4901.52:6418.56,4900.89:6419.41 #> sample1.67515 4916.40:6412.61,4912.15:6420.05,4910.45:6430.89 #> sample1.67521 4911.51:6397.95,4907.48:6400.71,4904.07:6407.30 #> sample1.67527 4929.57:6408.36,4924.69:6409.85,4921.29:6409.85 #> ...                                                       ... #> sample2.65063 4904.71:6399.65,4898.76:6401.35,4894.30:6407.94 #> sample2.65064 4905.77:6404.11,4906.20:6407.73,4907.05:6412.19 #> sample2.65067 4908.96:6395.61,4904.93:6399.44,4905.56:6403.26 #> sample2.65070 4919.59:6408.36,4915.98:6411.34,4915.76:6411.98 #> sample2.65071 4922.35:6404.54,4919.80:6407.94,4920.23:6413.46 rowData(se) #> DataFrame with 178 rows and 0 columns"},{"path":"https://sydneybiox.github.io/SpatialFeatures/articles/SpatialFeatures.html","id":"finish","dir":"Articles","previous_headings":"","what":"Finish","title":"An introduction to the SpatialFeatures Package","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.5 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] parallel  stats4    stats     graphics  grDevices utils     datasets  #> [8] methods   base      #>  #> other attached packages: #>  [1] ggplot2_3.5.1               SpatialFeatures_0.99.0      #>  [3] purrr_1.0.2                 dplyr_1.1.4                 #>  [5] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 #>  [7] Biobase_2.64.0              GenomicRanges_1.56.1        #>  [9] GenomeInfoDb_1.40.1         IRanges_2.38.1              #> [11] S4Vectors_0.42.1            BiocGenerics_0.50.0         #> [13] MatrixGenerics_1.16.0       matrixStats_1.4.1           #> [15] MoleculeExperiment_1.4.1    BiocStyle_2.32.1            #>  #> loaded via a namespace (and not attached): #>  [1] tidyselect_1.2.1         EBImage_4.46.0           farver_2.1.2             #>  [4] bitops_1.0-8             fastmap_1.2.0            RCurl_1.98-1.16          #>  [7] digest_0.6.37            lifecycle_1.0.4          terra_1.7-78             #> [10] magrittr_2.0.3           compiler_4.4.1           rlang_1.1.4              #> [13] sass_0.4.9               tools_4.4.1              utf8_1.2.4               #> [16] yaml_2.3.10              data.table_1.16.0        knitr_1.48               #> [19] labeling_0.4.3           S4Arrays_1.4.1           htmlwidgets_1.6.4        #> [22] bit_4.0.5                DelayedArray_0.30.1      abind_1.4-8              #> [25] BiocParallel_1.38.0      withr_3.0.1              desc_1.4.3               #> [28] grid_4.4.1               fansi_1.0.6              colorspace_2.1-1         #> [31] scales_1.3.0             cli_3.6.3                rmarkdown_2.28           #> [34] crayon_1.5.3             ragg_1.3.3               generics_0.1.3           #> [37] httr_1.4.7               rjson_0.2.23             cachem_1.1.0             #> [40] zlibbioc_1.50.0          BiocManager_1.30.25      XVector_0.44.0           #> [43] tiff_0.1-12              vctrs_0.6.5              Matrix_1.7-0             #> [46] jsonlite_1.8.8           bookdown_0.40            fftwtools_0.9-11         #> [49] bit64_4.0.5              systemfonts_1.1.0        jpeg_0.1-10              #> [52] magick_2.8.4             locfit_1.5-9.10          jquerylib_0.1.4          #> [55] glue_1.7.0               pkgdown_2.1.1            codetools_0.2-20         #> [58] gtable_0.3.5             UCSC.utils_1.0.0         munsell_0.5.1            #> [61] tibble_3.2.1             pillar_1.9.0             htmltools_0.5.8.1        #> [64] GenomeInfoDbData_1.2.12  R6_2.5.1                 textshaping_0.4.0        #> [67] evaluate_1.0.0           lattice_0.22-6           highr_0.11               #> [70] png_0.1-8                SpatialExperiment_1.14.0 bslib_0.8.0              #> [73] Rcpp_1.0.13              SparseArray_1.4.8        xfun_0.47                #> [76] fs_1.6.4                 pkgconfig_2.0.3"},{"path":"https://sydneybiox.github.io/SpatialFeatures/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Shila Ghazanfar. Author, maintainer, contributor. Guan Gui. Contributor.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ghazanfar S (2024). SpatialFeatures: Entropy-based subcellular supercellular features molecule-resolved spatial omics datasets. R package version 0.99.0, https://sydneybiox.github.io/SpatialFeatures/.","code":"@Manual{,   title = {SpatialFeatures: Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets},   author = {Shila Ghazanfar},   year = {2024},   note = {R package version 0.99.0},   url = {https://sydneybiox.github.io/SpatialFeatures/}, }"},{"path":"https://sydneybiox.github.io/SpatialFeatures/index.html","id":"spatialfeatures","dir":"","previous_headings":"","what":"Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets","title":"Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets","text":"R package incorprate features molecule-resolved spatial transcriptomics data. usage instructions package can found vignettes folder.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Entropy-based subcellular and supercellular features for molecule-resolved spatial omics datasets","text":"can install SpatialFeatures GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"SydneyBioX/SpatialFeatures\")"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"function retrieves counts matrix Molecule Experiment object based given assay type.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"","code":"CountsMatrix(me, assayName, nCores = 1, ...)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"Molecule Experiment object. assayName character string indicating assay type. Supported values include \"sub-sector\", \"sub-concentric\", \"sub-combo\", \"super-concentric\", \"super-combo\". nCores Number cores parallel processing (default 1) ... arguments passing MoleculeExperiment::countMolecules","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"counts matrix corresponding specified assay type.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/CountsMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract Counts Matrix from Molecule Experiment based on Assay Type — CountsMatrix","text":"","code":"# Assuming `data_obj` is your Molecule Experiment object # cm = CountsMatrix(data_obj, assayName = \"sub-sector\")"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"function computes entropy counts matrix MoleculeExperiment object based given assay type.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"","code":"EntropyMatrix(me, featureTypes, nCores = 1, ...)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"Molecule Experiment object. featureTypes character string specifying feature type. Supported values include \"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\". nCores Number cores ... arguments passing CountsMatrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"matrix representing entropy values corresponding given assay type.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropyMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the Entropy of a Counts Matrix — EntropyMatrix","text":"","code":"data(example_me) me <- loadBoundaries(me) ent <- EntropyMatrix(me, c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"), nCores = 1) lapply(ent, head, n = 4) #> $subsector #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     0.5623351     0.6931472     0.6365142     0.6931472 #> Acsbg1            0.6931472     0.6931472     0.6931472     0.0000000 #> Adamts2           0.0000000     0.0000000     0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0             0             0     0.0000000 #> Acsbg1                    0             0             0     0.6931472 #> Adamts2                   0             0             0     0.0000000 #> Adamtsl1                  0             0             0     0.0000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     1.5498260             0     0.6931472             0 #> Acsbg1            0.6931472             0     0.0000000             0 #> Adamts2           0.0000000             0     0.0000000             0 #> Adamtsl1          0.0000000             0     0.0000000             0 #>               sample2.65070 sample2.65071 #> 2010300C02Rik             0     0.0000000 #> Acsbg1                    0     0.6931472 #> Adamts2                   0     0.0000000 #> Adamtsl1                  0     0.0000000 #>  #> $subconcentric #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     0.5623351     0.6931472     0.6365142             0 #> Acsbg1            0.6931472     0.0000000     0.6931472             0 #> Adamts2           0.0000000     0.0000000     0.0000000             0 #> Adamtsl1          0.0000000     0.0000000     0.0000000             0 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0             0             0             0 #> Acsbg1                    0             0             0             0 #> Adamts2                   0             0             0             0 #> Adamtsl1                  0             0             0             0 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     1.2770343             0     0.6931472             0 #> Acsbg1            0.6931472             0     0.0000000             0 #> Adamts2           0.0000000             0     0.0000000             0 #> Adamtsl1          0.0000000             0     0.0000000             0 #>               sample2.65070 sample2.65071 #> 2010300C02Rik             0             0 #> Acsbg1                    0             0 #> Adamts2                   0             0 #> Adamtsl1                  0             0 #>  #> $supersector #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik             0      1.332179     0.6931472     0.6931472 #> Acsbg1                    0      0.000000     0.6931472     0.6931472 #> Adamts2                   0      0.000000     0.0000000     0.0000000 #> Adamtsl1                  0      0.000000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik             0     0.5623351      1.039721     0.5982696 #> Acsbg1                    0     0.0000000      0.000000     0.9502705 #> Adamts2                   0     0.0000000      0.000000     0.0000000 #> Adamtsl1                  0     0.0000000      0.000000     0.0000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik      0.000000     0.6931472             0     0.0000000 #> Acsbg1             1.559581     1.0114043             0     0.6931472 #> Adamts2            0.000000     0.0000000             0     0.0000000 #> Adamtsl1           0.000000     0.0000000             0     0.0000000 #>               sample2.65070 sample2.65071 #> 2010300C02Rik     0.0000000     0.0000000 #> Acsbg1            0.5623351     0.6365142 #> Adamts2           0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000 #>  #> $superconcentric #>               sample1.67500 sample1.67512 sample1.67515 sample1.67521 #> 2010300C02Rik     1.5607104       1.05492     0.6931472     0.0000000 #> Acsbg1            0.6931472       0.00000     0.6931472     0.6931472 #> Adamts2           0.0000000       0.00000     0.0000000     0.0000000 #> Adamtsl1          0.0000000       0.00000     0.0000000     0.0000000 #>               sample1.67527 sample2.65043 sample2.65044 sample2.65051 #> 2010300C02Rik     0.0000000      1.039721      1.386294      1.549826 #> Acsbg1            0.6931472      0.000000      0.000000      1.054920 #> Adamts2           0.0000000      0.000000      0.000000      0.000000 #> Adamtsl1          0.0000000      0.000000      0.000000      0.000000 #>               sample2.65055 sample2.65063 sample2.65064 sample2.65067 #> 2010300C02Rik     0.6931472     0.6931472      1.386294     0.0000000 #> Acsbg1            1.3208883     1.3296613      0.000000     0.6931472 #> Adamts2           0.0000000     0.0000000      0.000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000      0.000000     0.0000000 #>               sample2.65070 sample2.65071 #> 2010300C02Rik     0.6931472     0.0000000 #> Acsbg1            0.6931472     0.6365142 #> Adamts2           0.0000000     0.0000000 #> Adamtsl1          0.0000000     0.0000000 #>"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"function takes list data frames Molecule Experiment object constructs SingleCellExperiment object specified data structure.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"","code":"EntropySingleCellExperiment(   df_list,   me,   includeCounts = FALSE,   concatenateFeatures = FALSE,   nCores = 1 )"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"df_list list data frames, containing assay data. Molecule Experiment object. includeCounts logical (default FALSE) whether include gene counts features concatenateFeatures logical whether concatenate features single assay (default FALSE). FALSE output SE object multiple assays nCores Number cores (default 1)","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"SingleCellExperiment object.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/EntropySingleCellExperiment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a SingleCellExperiment Object from a List of Data Frames — EntropySingleCellExperiment","text":"","code":"data(example_me) me <- loadBoundaries(me) ent <- EntropyMatrix(me, c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"), nCores = 1) se <- EntropySingleCellExperiment(ent, me) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(4): subsector subconcentric supersector superconcentric #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0):"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/GenerateFeatureData.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","title":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","text":"comprehensive function processes given data () returns feature data based multiple assay types. supported assays encapsulated within function include: Sub-sector polygons Sub-concentric polygons Sub-combo polygons Super-concentric polygons Super-combo polygons assays represent various spatial subdivisions transformations, addressing unique feature characteristics. results assay combined returned list dataframes.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/GenerateFeatureData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","text":"","code":"GenerateFeatureData(   me,   featureTypes = c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"),   k = 5 )"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/GenerateFeatureData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","text":"input data object. object contains spatial information, typically regarding segments regions interest. featureTypes Character vector containing feature types calculate. k numeric value indicating scaling factor concentric polygons. Defaults 5.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/GenerateFeatureData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate Feature Data Based on Assay Type Combining Various Polygon Assays — GenerateFeatureData","text":"list containing dataframes assay type: subsector: Feature data sub-sector polygons. subconcentric: Feature data sub-concentric polygons. supersector: Feature data super-sector polygons. superconcentric: Feature data super-concentric polygons.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/annuli_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","title":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","text":"Convert cumulative counts concentric polygons annuli polygon counts","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/annuli_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","text":"","code":"annuli_counts(mat)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/annuli_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","text":"mat matrix cumulative counts.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/annuli_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert cumulative counts in concentric polygons to annuli polygon counts — annuli_counts","text":"matrix annuli polygon counts.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_centroids.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate centroids from boundaries — calculate_centroids","title":"Calculate centroids from boundaries — calculate_centroids","text":"Calculate centroids boundaries","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_centroids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate centroids from boundaries — calculate_centroids","text":"","code":"calculate_centroids(df_boundary)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_centroids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate centroids from boundaries — calculate_centroids","text":"df_boundary data frame boundaries.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_centroids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate centroids from boundaries — calculate_centroids","text":"data frame centroids.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_entropy.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate entropy from a probability vector — calculate_entropy","title":"Calculate entropy from a probability vector — calculate_entropy","text":"Calculate entropy probability vector","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_entropy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate entropy from a probability vector — calculate_entropy","text":"","code":"calculate_entropy(p)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_entropy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate entropy from a probability vector — calculate_entropy","text":"p numeric vector probabilities.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/calculate_entropy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate entropy from a probability vector — calculate_entropy","text":"calculated entropy value.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/compute_cell_entropy.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute entropy for a given matrix — compute_cell_entropy","title":"Compute entropy for a given matrix — compute_cell_entropy","text":"Compute entropy given matrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/compute_cell_entropy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute entropy for a given matrix — compute_cell_entropy","text":"","code":"compute_cell_entropy(cell_segments_mat)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/compute_cell_entropy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute entropy for a given matrix — compute_cell_entropy","text":"cell_segments_mat matrix compute entropy .","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/compute_cell_entropy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute entropy for a given matrix — compute_cell_entropy","text":"vector entropy values.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/countsprop.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate prop for entropy — countsprop","title":"Calculate prop for entropy — countsprop","text":"Calculate prop entropy","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/countsprop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate prop for entropy — countsprop","text":"","code":"countsprop(counts)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/countsprop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate prop for entropy — countsprop","text":"counts vector integers","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/countsprop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate prop for entropy — countsprop","text":"proportion","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_sub.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a scaled data frame — create_scaled_df_sub","title":"Create a scaled data frame — create_scaled_df_sub","text":"Create scaled data frame","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_sub.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a scaled data frame — create_scaled_df_sub","text":"","code":"create_scaled_df_sub(s, df_circle, k = 5)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_sub.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a scaled data frame — create_scaled_df_sub","text":"s numeric scaling factor. df_circle data frame scale. k numeric value, defaulting 8.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_sub.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a scaled data frame — create_scaled_df_sub","text":"scaled data frame.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_super.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a scaled data frame — create_scaled_df_super","title":"Create a scaled data frame — create_scaled_df_super","text":"Create scaled data frame","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_super.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a scaled data frame — create_scaled_df_super","text":"","code":"create_scaled_df_super(s, df_circle, k = 5)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_super.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a scaled data frame — create_scaled_df_super","text":"s numeric scaling factor. df_circle data frame scale. k numeric value, defaulting 8.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_scaled_df_super.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a scaled data frame — create_scaled_df_super","text":"scaled data frame.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sector_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Create sector data frame from circle data — create_sector_df","title":"Create sector data frame from circle data — create_sector_df","text":"function takes data frame circle data segment IDs locations, returns data frame sectors scaled coordinates.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sector_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create sector data frame from circle data — create_sector_df","text":"","code":"create_sector_df(df)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sector_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create sector data frame from circle data — create_sector_df","text":"df data frame containing circle data segment IDs, x y locations.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sector_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create sector data frame from circle data — create_sector_df","text":"data frame coordinates sector.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Create sectors from a given data frame — create_sectors","title":"Create sectors from a given data frame — create_sectors","text":"Create sectors given data frame","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create sectors from a given data frame — create_sectors","text":"","code":"create_sectors(df)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create sectors from a given data frame — create_sectors","text":"df data frame create sectors .","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/create_sectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create sectors from a given data frame — create_sectors","text":"data frame sectors.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract boundaries from a given object — extract_boundaries","title":"Extract boundaries from a given object — extract_boundaries","text":"Extract boundaries given object","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract boundaries from a given object — extract_boundaries","text":"","code":"extract_boundaries(me)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract boundaries from a given object — extract_boundaries","text":"object extract boundaries .","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract boundaries from a given object — extract_boundaries","text":"data frame extracted boundaries.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries_and_centroids.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","title":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","text":"Extract boundaries calculate centroids","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries_and_centroids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","text":"","code":"extract_boundaries_and_centroids(me)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries_and_centroids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","text":"object process.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_boundaries_and_centroids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract boundaries and calculate centroids — extract_boundaries_and_centroids","text":"list containing data frame boundaries data frame centroids.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_cell_segments.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","title":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","text":"Extract submatrix corresponding segment matrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_cell_segments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","text":"","code":"extract_cell_segments(mat, cell)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_cell_segments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","text":"mat matrix process. cell character string indicating segment extract.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/extract_cell_segments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract a submatrix corresponding to a segment from a matrix — extract_cell_segments","text":"submatrix provided matrix.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate scale factors for all values of k — generate_scale_factors_all","title":"Generate scale factors for all values of k — generate_scale_factors_all","text":"Generate scale factors values k","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate scale factors for all values of k — generate_scale_factors_all","text":"","code":"generate_scale_factors_all(k)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate scale factors for all values of k — generate_scale_factors_all","text":"k numeric value.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate scale factors for all values of k — generate_scale_factors_all","text":"vector scale factors.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all_outside.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","title":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","text":"Generate scale factors outside values ks","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all_outside.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","text":"","code":"generate_scale_factors_all_outside(k)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all_outside.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","text":"k numeric value.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/generate_scale_factors_all_outside.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate scale factors for all outside values of ks — generate_scale_factors_all_outside","text":"vector scale factors outside values.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/get_cells.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract unique segments from matrix column names — get_cells","title":"Extract unique segments from matrix column names — get_cells","text":"Extract unique segments matrix column names","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/get_cells.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract unique segments from matrix column names — get_cells","text":"","code":"get_cells(mat)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/get_cells.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract unique segments from matrix column names — get_cells","text":"mat matrix process.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/get_cells.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract unique segments from matrix column names — get_cells","text":"character vector unique segments.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":null,"dir":"Reference","previous_headings":"","what":"Load Boundaries to Molecule Experiment Object — loadBoundaries","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"function takes Molecule Experiment () object input enriches boundary data variety assays. currently supported assays : Sub-sector polygons Sub-concentric polygons Super-sector polygons Super-concentric polygons function internally processes assay, extracts respective boundary information, updates original object new data.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"","code":"loadBoundaries(me, ...)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"MoleculeExperiment () object ... arguments passed GenerateFeatureData","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"enriched Molecule Experiment () object includes boundary information supported assays.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/loadBoundaries.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load Boundaries to Molecule Experiment Object — loadBoundaries","text":"","code":"data(example_me) me <- loadBoundaries(me) me #> MoleculeExperiment class #>  #> molecules slot (1): detected #> - detected: #> samples (2): sample1 sample2 #> -- sample1: #> ---- features (137): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (962) #> ---- location range: [4900,4919.98] x [6400.02,6420] #> -- sample2: #> ---- features (143): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> ---- molecules (777) #> ---- location range: [4900.01,4919.98] x [6400.16,6419.97] #>  #>  #> boundaries slot (5): cell subsector subconcentric supersector #>   superconcentric #> - cell: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (5): 67500 67512 67515 67521 67527 #> -- sample2: #> ---- segments (9): 65043 65044 ... 65070 65071 #> - subsector: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (60): 67500_01 67500_02 ... 67527_11 67527_12 #> -- sample2: #> ---- segments (108): 65043_01 65043_02 ... 65071_11 65071_12 #> - subconcentric: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (30): 67500_01 67500_02 ... 67527_05 67527_06 #> -- sample2: #> ---- segments (54): 65043_01 65043_02 ... 65071_05 65071_06 #> - supersector: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (55): 67500_01 67500_02 ... 67527_10 67527_11 #> -- sample2: #> ---- segments (99): 65043_01 65043_02 ... 65071_10 65071_11 #> - superconcentric: #> samples (2): sample1 sample2 #> -- sample1: #> ---- segments (35): 67500_01 67500_02 ... 67527_06 67527_07 #> -- sample2: #> ---- segments (63): 65043_01 65043_02 ... 65071_06 65071_07"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/make_assay_data.html","id":null,"dir":"Reference","previous_headings":"","what":"make assay data — make_assay_data","title":"make assay data — make_assay_data","text":"make assay data","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/make_assay_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"make assay data — make_assay_data","text":"","code":"make_assay_data(df_list, concatenateFeatures = FALSE)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/make_assay_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"make assay data — make_assay_data","text":"df_list list data frames concatenateFeatures logical whether concatenate features (default FALSE)","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/make_assay_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"make assay data — make_assay_data","text":"concatenateFeatures == TRUE, single data frame, otherwise list containing data frames","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/matrix_entropy.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute entropy for the entire matrix — matrix_entropy","title":"Compute entropy for the entire matrix — matrix_entropy","text":"Compute entropy entire matrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/matrix_entropy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute entropy for the entire matrix — matrix_entropy","text":"","code":"matrix_entropy(mat, nCores = 1)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/matrix_entropy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute entropy for the entire matrix — matrix_entropy","text":"mat matrix compute entropy . nCores Number cores","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/matrix_entropy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute entropy for the entire matrix — matrix_entropy","text":"data frame entropy values matrix.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/me.html","id":null,"dir":"Reference","previous_headings":"","what":"Example MoleculeExperiment data — me","title":"Example MoleculeExperiment data — me","text":"tiny object containing cells molecules","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/me.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example MoleculeExperiment data — me","text":"","code":"data(example_me, package = 'SpatialFeatures')"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/me.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example MoleculeExperiment data — me","text":"MoleculeExperiment object.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/modify_area_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify the area_id format — modify_area_id","title":"Modify the area_id format — modify_area_id","text":"function takes area_id string modifies last segment single-digit number 1 9 adding leading zero.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/modify_area_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify the area_id format — modify_area_id","text":"","code":"modify_area_id(id)"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/modify_area_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify the area_id format — modify_area_id","text":"id string representing area_id.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/modify_area_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify the area_id format — modify_area_id","text":"string modified area_id format.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate SpatialFeatures — spatialFeatures","title":"Calculate SpatialFeatures — spatialFeatures","text":"function takes MoleculeExperiment () object input calculates new molecule-based spatial features according following segmentations: Sub-sector polygons Sub-concentric polygons Super-sector polygons Super-concentric polygons function 3 key steps, 1. adds new boundaries object according subcellular supercellular segmentations, 2. calculates entropy cell featureType combinations, 3. combines entropy values SingleCellExperiment object.","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate SpatialFeatures — spatialFeatures","text":"","code":"spatialFeatures(   me,   featureTypes = c(\"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\"),   k = 5,   nCores = 1,   includeCounts = FALSE,   concatenateFeatures = FALSE,   ... )"},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate SpatialFeatures — spatialFeatures","text":"MoleculeExperiment () object featureTypes character string specifying feature type. Supported values include \"subsector\", \"subconcentric\", \"supersector\", \"superconcentric\". k numeric value indicating number polygons calculate entropy (default 5) nCores number cores parallel processing (default 1) includeCounts logical (default FALSE) whether include gene counts features concatenateFeatures logical whether concatenate features single assay (default FALSE). FALSE output SE object multiple assays ... arguments passed loadBoundaries EntropyMatrix","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate SpatialFeatures — spatialFeatures","text":"SingleCellExperiment object containing spatialFeatures assay cell-level colData","code":""},{"path":"https://sydneybiox.github.io/SpatialFeatures/reference/spatialFeatures.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate SpatialFeatures — spatialFeatures","text":"","code":"data(example_me) se <- spatialFeatures(me) se #> class: SingleCellExperiment  #> dim: 178 14  #> metadata(0): #> assays(4): subsector subconcentric supersector superconcentric #> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2 #> rowData names(0): #> colnames(14): sample1.67500 sample1.67512 ... sample2.65070 #>   sample2.65071 #> colData names(5): Cell Sample_id x_central y_central boundaries #> reducedDimNames(0): #> mainExpName: NULL #> altExpNames(0):"},{"path":"https://sydneybiox.github.io/SpatialFeatures/news/index.html","id":"spatialfeatures-v0990-2024-09-19","dir":"Changelog","previous_headings":"","what":"SpatialFeatures v0.99.0 (2024-09-19)","title":"SpatialFeatures v0.99.0 (2024-09-19)","text":"Submitted Bioconductor.","code":""}]