plotGeneExpressionInBackgroundHist: Histogram All Genes' Expression Level and a Highlighted Gene

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

Histogram All Genes' Expression Level and a Highlighted Gene

Description

Shows a comparison of the expression level of the chose gene to all genes. Very useful to see if the gene has a meaningful expression level. This function generates a histogram to visualize the expression level distribution of a specified gene across all cells in a Seurat object. It highlights the position of the gene of interest within the overall distribution.

Usage

plotGeneExpressionInBackgroundHist(
  gene = "TOP2A",
  obj = combined.obj,
  assay = "RNA",
  slot = c("counts", "data")[2],
  w = 7,
  h = 4,
  ...
)

Arguments

gene	The gene of interest for which the expression level distribution is to be plotted. Default: 'TOP2A'.
obj	A Seurat object containing the expression data. Default: The first Seurat object in ls.Seurat.
assay	The assay from which to retrieve the expression data. Default: "RNA".
slot	The slot in the Seurat object from which to retrieve the expression data. Options include "counts" for raw counts and "data" for normalized (and possibly log-transformed) data. Default: "data".
w	The width of the plot. Default: 7.
h	The height of the plot. Default: 4.
...	Any other parameter that can be passed to the internally called functions.

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