plot_GEboxplot: scClustViz plot: Compare gene expression across clusters

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

scClustViz plot: Compare gene expression across clusters

Description

This function generates boxplots comparing normalized gene abundance across all clusters.

Usage

plot_GEboxplot(nge, sCVd, gene, geneName, opts = c("sct", "dr"))

Arguments

nge	The gene expression matrix, see getExprs.
sCVd	The sCVdata object.
gene	The gene to display.
geneName	Optional. A named character vector of length one. The element is the full gene name, and the name is the gene symbol.
opts	Default=c("sct","dr"). A character vector with plotting options. If it includes "sct", data points will be overlaid as a jitter over the boxplot. If it includes "dr", detection rate per cluster will be plotted as a small black bar over each boxplot, with the corresponding axis on the right.

Examples

## Not run: 
plot_GEboxplot(getExpr(input_data_obj),
               sCVd=sCVdata,
               gene="Actb")

## End(Not run)

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.