compareVarFeaturesAndRanks: Compare variable features and their ranks in two Seurat...

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

Compare variable features and their ranks in two Seurat objects.

Description

This function compares variable features (genes) between two Seurat objects, reporting the number of genes in each, the percentage of common genes, the percentage of unique genes in each object, and the similarity in the ranking of overlapping genes using Spearman's rank correlation coefficient. Optionally, it can also generate a scatterplot of the ranks of common genes using ggpubr's ggscatter. The function returns the common genes and the Spearman's rank correlation coefficient.

Usage

compareVarFeaturesAndRanks(
  obj1 = NULL,
  obj2 = NULL,
  cor.plot = TRUE,
  save.plot = TRUE,
  plot_venn = TRUE,
  suffix = NULL,
  ...
)

Arguments

obj1	The first Seurat object for comparison. Default: NULL.
obj2	The second Seurat object for comparison. Default: NULL.
cor.plot	An optional boolean indicating whether to generate a scatterplot of the ranks of common genes. Default: FALSE.
save.plot	save.plot
plot_venn	plot_venn
suffix	suffix

Value

A list containing the common genes and Spearman's rank correlation coefficient. If cor.plot is TRUE, a scatterplot is also generated.

Examples

# Assuming obj1 and obj2 are Seurat objects
result <- compareVarFeaturesAndRanks(obj1, obj2, cor.plot = TRUE)

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