plotGeneExprHistAcrossCells: Histogram of Gene / Geneset Aggregate Expression Across Cells

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

Histogram of Gene / Geneset Aggregate Expression Across Cells

Description

Creates and optionally saves a histogram showing expression levels of specified genes within a Seurat object. Provides options for aggregate gene expression, expression threshold filtering, and quantile clipping for count data.

Usage

plotGeneExprHistAcrossCells(
  genes = c("MALAT1", "MT-CO1", "MT-CO2", "MT-CYB", "TMSB4X", "KAZN"),
  obj = combined.obj,
  assay = "RNA",
  layerX = "data",
  thr_expr = 10,
  suffix = NULL,
  prefix = NULL,
  plotname = c("Summed Gene-set Expression -", "Expression of"),
  xlab = paste0("Expression -log10(Summed UMIs @", layerX, ")"),
  return_cells_passing = TRUE,
  clip_count_qtl_thr = 0.99,
  log10_counts = TRUE,
  return_quantile,
  w = 9,
  h = 5,
  show_plot = TRUE,
  ...
)

Arguments

genes	Vector of gene names to include in the analysis; Default: c("MALAT1", "MT-CO1").
obj	Seurat object to analyze; Default: combined.obj.
assay	Assay to use from the Seurat object; Default: "RNA".
layerX	Data slot to use ('data' or 'counts'); Default: "data".
thr_expr	Expression threshold for highlighting in the plot; Default: 10.
suffix	Additional text to append to the plot title; Default: NULL.
prefix	Additional text to prepend to the plot title; Default: NULL.
xlab	Label for the x-axis; Default: "log10(Summed UMI count @data)".
return_cells_passing	If TRUE, returns count of cells exceeding the expression threshold; Default: TRUE.
clip_count_qtl_thr	Quantile threshold for clipping if using count data; Default: 0.95. Needed for visualization (to avoid x axis compression).
log10_counts	If TRUE, log10-transforms the COUNT expression values; Default: TRUE.
return_quantile	If TRUE, returns cell count exceeding the quantile threshold; Default: FALSE.
w	Width of the plot in inches; Default: 9.
h	Height of the plot in inches; Default: 5.
show_plot	If TRUE, displays the generated plot; Default: TRUE.
...	Additional arguments for customization.

Value

Depending on the parameters, can return a ggplot object, the number of cells passing the expression threshold, or the number of cells exceeding the quantile threshold.

Depending on the parameters, can return a ggplot object, the number of cells passing the expression threshold, or the number of cells exceeding the quantile threshold.

Examples

## Not run: 
plotGeneExprHistAcrossCells(obj = yourSeuratObject, genes = c("GeneA", "GeneB"))

## End(Not run)

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