plotQUMAPsInAFolder: Plot qUMAPs for Genes in a Folder

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Plot qUMAPs for Genes in a Folder

Description

This function plots qUMAPs for a specified set of genes, storing the results in a specified folder. If no folder name is provided, it defaults to using the gene set name.

Usage

plotQUMAPsInAFolder(
  genes,
  obj = combined.obj,
  foldername = NULL,
  intersectionAssay = DefaultAssay(obj),
  plot.reduction = "umap",
  ...
)

Arguments

genes	A vector of gene names to be plotted.
obj	An object containing the UMAP and gene data. Default: combined.obj.
foldername	The name of the folder where the plots will be saved. If NULL, the gene set name is used. Default: NULL.
intersectionAssay	The assay slot to use for intersection. Default: 'RNA'.
plot.reduction	The type of reduction to plot. Default: 'umap'.
...	Additional arguments passed to plotting and directory creation functions.

Value

Invisible. The function generates plots and saves them in the specified folder.

Examples

plotQUMAPsInAFolder(
  genes = c("Gene1", "Gene2"), obj = combined.obj,
  foldername = "MyGenePlots", intersectionAssay = "RNA",
  plot.reduction = "umap"
)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.