minor changes

sipss · Feb 21, 2024 · cccb778 · cccb778
1 parent 1ff18e7
commit cccb778
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/R/align_ip_GCIMSDataset.R → R/align_ip-GCIMSDataset.R b/R/align_ip_GCIMSDataset.R → R/align_ip-GCIMSDataset.R
diff --git a/R/align_ip_GCIMSSample.R → R/align_ip-GCIMSSample.R b/R/align_ip_GCIMSSample.R → R/align_ip-GCIMSSample.R
diff --git a/vignettes/introduction-to-gcims.Rmd b/vignettes/introduction-to-gcims.Rmd
@@ -192,9 +192,9 @@ to_plot <- dplyr::bind_rows(
   Smoothed = as.data.frame(one_ims_smoothed),
   .id = "Status"
 )
-plotly::ggplotly(ggplot(to_plot) +
+plot_interactive((ggplot(to_plot) +
   geom_line(aes(x = drift_time_ms, y = intensity, colour = Status)) +
-  labs(x = "Drift time (ms)", y = "Intensity (a.u.)"))
+  labs(x = "Drift time (ms)", y = "Intensity (a.u.)")))
 ```
 
 ```{r}
@@ -208,7 +208,7 @@ to_plot <- dplyr::bind_rows(
   Smoothed = as.data.frame(one_chrom_smoothed),
   .id = "Status"
 )
-plotly::ggplotly(ggplot(to_plot) +
+plot_interactive(ggplot(to_plot) +
   geom_line(aes(x = retention_time_s, y = intensity, colour = Status)) +
   labs(x = "Retention time (s)", y = "Intensity (a.u.)"))
 ```
@@ -390,7 +390,7 @@ ket1 <- findPeaks(
 
 ```{r}
 peak_list_ket1 <- peaks(ket1)
-plotly::ggplotly(plot(ket1) +
+plot_interactive(plot(ket1) +
   overlay_peaklist(peak_list_ket1, color_by = "PeakID"))
 ```
 
@@ -420,7 +420,7 @@ ket2 <- dataset$getSample("Ketones2")
 ```
 
 ```{r}
-plotly::ggplotly(plot(ket2) +
+plot_interactive(plot(ket2) +
   overlay_peaklist(peaks(ket2)) )
 ```
 
@@ -429,7 +429,7 @@ Or plot all the peaks from all the dataset together, overlayed on a single sampl
 ```{r}
 plt <- plot(ket2) +
   overlay_peaklist(peaks(dataset), color_by = "SampleID")
-plotly::ggplotly(plt)
+plot_interactive(plt)
 ```
 
 # Clustering
@@ -454,13 +454,13 @@ peak_list_clustered <- peak_clustering$peak_list_clustered
 ```{r }
 plt <- plot(ket2) +
   overlay_peaklist(peak_list_clustered, color_by = "SampleID")
-plotly::ggplotly(plt)
+plot_interactive(plt)
 ```
 
 ```{r}
 plt <- plot(ket2) +
   overlay_peaklist(dplyr::filter(peak_list_clustered, !is.na(cluster)), color_by = "cluster")
-plotly::ggplotly(plt)
+plot_interactive(plt)
 ```
 
 The resulting cluster sizes (median position of individual clusters) is not a good reference
@@ -469,7 +469,7 @@ for integration. We are working on this.
 ```{r}
 plt <- plot(ket2) +
   overlay_peaklist(peak_clustering$cluster_stats, color_by = "cluster")
-plotly::ggplotly(plt)
+plot_interactive(plt)
 ```
 
 # Baseline correction
@@ -494,7 +494,7 @@ to_plot <- data.frame(
   Intensity = intensity(one_ims_spec),
   Baseline = baseline(one_ims_spec)
 )
-plotly::ggplotly(ggplot(to_plot) +
+plot_interactive(ggplot(to_plot) +
   geom_line(aes(x = drift_time_ms, y = Intensity), color = "red") +
   geom_line(aes(x = drift_time_ms, y = Baseline), color = "blue") +
   labs(x = "Drift time (ms)", y = "Intensity (a.u.)"))