nf sizes.highlight

vertesy · Nov 25, 2024 · 80fd6d6 · 80fd6d6
1 parent d81bde2
commit 80fd6d6
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R
@@ -2446,7 +2446,7 @@ removeResidualSmallClusters <- function(
     is.numeric(max.cells), max.cells > 0,
     is.logical(plot.removed)
   )
-
+  message("First, consider using RelabelSmallCategories() instead, to relabel small clusters.")
 
   META <- obj@meta.data
   all.cells <- rownames(META)

diff --git a/R/Seurat.Utils.Visualization.R b/R/Seurat.Utils.Visualization.R
@@ -2215,6 +2215,8 @@ qUMAP <- function(
 #' @param palette Color palette for generating cluster colors; Default: 'glasbey'.
 #' @param highlight.clusters Specific clusters to be highlighted; optional; Default: NULL.
 #' @param cells.highlight Specific cells to be highlighted; optional; Default: NULL.
+#' @param cols.highlight Color for highlighted cells; Default: 'red'.
+#' @param sizes.highlight Size of highlighted cells; Default: 1.
 #' @param label Show cluster labels; Default: `TRUE`.
 #' @param repel Repel labels to avoid overlap; Default: `TRUE`.
 #' @param legend Show legend; Default: opposite of `label`.
@@ -2637,6 +2639,7 @@ multiFeaturePlot.A4 <- function(
 #' @param nr.Col Number of columns in the plot grid. Default: 2.
 #' @param nr.Row Number of rows in the plot grid. Default: 4.
 #' @param cex Size of the text in the plot, calculated based on the number of rows and columns. Default: Calculated value.
+#' @param sizes.highlight Size of highlighted cells; Default: 1.
 #' @param subdir Logical flag indicating whether to create a subdirectory for the plots. Default: `TRUE`.
 #' @param prefix Optional prefix for the plot file names. Default: `NULL`.
 #' @param suffix Optional suffix for the plot file names. Default: `NULL`.
@@ -2669,6 +2672,7 @@ multiSingleClusterHighlightPlots.A4 <- function(
     colors = c("grey", "red"),
     nr.Col = 2, nr.Row = 4,
     cex = round(0.1 / (nr.Col * nr.Row), digits = 2),
+    sizes.highlight = 1,
     subdir = TRUE,
     prefix = NULL, suffix = NULL,
     background_col = "white",
@@ -2728,7 +2732,9 @@ multiSingleClusterHighlightPlots.A4 <- function(
       plot.list[[j]] <- clUMAP(
         ident = ident, obj = obj,
         highlight.clusters = cl, label = FALSE, legend = FALSE, save.plot = FALSE,
-        plotname = plotname, cols = colors, h = h, w = w, ...
+        plotname = plotname, cols = colors,
+        sizes.highlight = sizes.highlight,
+        h = h, w = w, ...
       )
     } # for j