From 80fd6d6c671c4a9bdc42d6199ad03e326b3a48eb Mon Sep 17 00:00:00 2001 From: vertesy Date: Mon, 25 Nov 2024 19:45:16 +0100 Subject: [PATCH] nf sizes.highlight --- R/Seurat.Utils.R | 2 +- R/Seurat.Utils.Visualization.R | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R index 2f46e44..22715e5 100644 --- 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 index 65760fd..36b8889 100644 --- 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