Improved examples and example data to ensure no errors.

SydneyBioX · Aug 27, 2024 · 6068101 · 6068101
1 parent 22c201b
commit 6068101
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Showing 10 changed files with 17 additions and 19 deletions.
diff --git a/R/clustSIGNAL.R b/R/clustSIGNAL.R
@@ -28,9 +28,9 @@
 #'
 #' names(colData(spe))
 #' # identify the column names with cell and sample labels
-#' samples = "embryo"
+#' samples = "sample_id"
 #' cells = "uniqueID"
-#' res_list <- clustSIGNAL(spe, samples, cells, dimRed = "PCA", outputs = "c")
+#' res_list <- clustSIGNAL(spe, samples, cells, outputs = "c")
 #'
 #'
 #' @export

diff --git a/R/clustering.R b/R/clustering.R
@@ -11,15 +11,14 @@
 #' @examples
 #' data(mouseEmbryo2)
 #'
-#' # for non-spatial clustering of normalised counts
+#' spe <- scater::runPCA(spe)
+#'
+#' # reclust = FALSE for non-spatial clustering of normalised counts
+#' # reclust = TRUE for non-spatial clustering of adaptively smoothed counts
 #' spe <- nsClustering(spe, dimRed = "PCA", reclust = FALSE)
 #' head(spe$nsCluster)
 #' head(spe$nsSubcluster)
 #'
-#' # for non-spatial clustering of adaptively smoothed counts
-#' spe <- nsClustering(spe, dimRed = "PCA", reclust = TRUE)
-#' head(spe$reCluster)
-#'
 #' @export
 
 #### Non-spatial clustering

diff --git a/R/entropyMeasure.R b/R/entropyMeasure.R
@@ -13,7 +13,7 @@
 #' @examples
 #' data(mouseEmbryo2)
 #'
-#' # requires list of containing cluster proportions of each region (regXclust),
+#' # requires list containing cluster proportions of each region (regXclust),
 #' # generated using the neighbourDetect() function
 #' spe <- entropyMeasure(spe, cells = "uniqueID", regXclust, threads = 1)
 #' head(spe$entropy)

diff --git a/R/neighborDetect.R b/R/neighborDetect.R
@@ -18,7 +18,7 @@
 #' @examples
 #' data(mouseEmbryo2)
 #'
-#' out_list <- neighbourDetect(spe, samples = "embryo", NN = 30, cells = "uniqueID", sort = TRUE)
+#' out_list <- neighbourDetect(spe, samples = "sample_id", NN = 30, cells = "uniqueID", sort = TRUE)
 #' names(out_list)
 #'
 #' @export

diff --git a/data/mouseEmbryo2.rda b/data/mouseEmbryo2.rda
diff --git a/man/clustSIGNAL.Rd b/man/clustSIGNAL.Rd
diff --git a/man/entropyMeasure.Rd b/man/entropyMeasure.Rd
diff --git a/man/neighbourDetect.Rd b/man/neighbourDetect.Rd
diff --git a/man/nsClustering.Rd b/man/nsClustering.Rd
diff --git a/vignettes/1_seqFISH_mouseEmbryo.Rmd b/vignettes/1_seqFISH_mouseEmbryo.Rmd
@@ -51,7 +51,7 @@ To run clustSIGNAL, we need the column names of sample and cell labels in the co
 
 ```{r}
 set.seed(100)
-samples = "embryo"
+samples = "sample_id"
 cells = "uniqueID"
 res_emb = clustSIGNAL(spe, samples, cells, outputs = "a")
 ```