PercentInTranscriptome: Gene Expression as Fraction of Total UMI Counts

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

Gene Expression as Fraction of Total UMI Counts

Description

This function computes and visualizes gene expression levels as a fraction of total UMI (Unique Molecular Identifier) counts across all genes in a Seurat object. It aims to highlight the relative contribution of the most highly expressed genes to the overall transcriptome.

Usage

PercentInTranscriptome(
  obj = combined.obj,
  assay = DefaultAssay(obj),
  n.genes.barplot = 25,
  width.barplot = round(n.genes.barplot/4),
  ...
)

Arguments

obj	A Seurat object containing gene expression data.
n.genes.barplot	The number of top genes to be displayed in the final barplot, showing their expression as a percentage of the total UMIs. Default: 25.
width.barplot	The width of the barplot that visualizes the highest expressed genes. Default: a quarter of n.genes.barplot.

Value

The same Seurat object passed as input, but with an additional list in the ⁠@misc⁠ slot named 'TotalReadFraction' that contains the relative total expression of each gene as a fraction of total UMIs.

Examples

## Not run: 
combined.obj <- PercentInTranscriptome(combined.obj)

## End(Not run)

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