plotGeneExpression-scRNAseq: plotGeneExpression

In ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

plotGeneExpression

Description

The function saves a t-SNE plot colored by expression of a given gene.

Usage

plotGeneExpression(theObject, geneName,
palette=c("grey","red", "#7a0f09", "black"), returnPlot=FALSE,
            tSNEpicture=1, savePlot=FALSE, alpha=1, limits=NA,
            pointSize=1, width=6, height=5, plotPDF=TRUE, silentPlot=FALSE)

Arguments

theObject	A scRNAseq object with the top markers retrieved. See ?retrieveTopClustersMarkers.
geneName	Name of the gene to highlight on the t-SNE plot.
palette	Color palette for the expression levels.
returnPlot	If TRUE, returns a ggplot object of the tSNE. Default = FALSE.
tSNEpicture	Number of the tSNE picture that you want to use for plotting the gene expression. Default = 1.
savePlot	If TRUE, save the tSNE in pdf or png format. Default=FALSE.
alpha	Opacity of the points of the plot. Default = 1.
limits	Range of the gene expression shown in the legend. Default = NA. See details.
pointSize	Size of the points on the tSNE. Default = 1.
width	Width of the plot. Default = 6.
height	Height of the plot. Default = 5.
plotPDF	If TRUE export tSNE in pdf format, if FALSE export it in png format. Default=TRUE.
silentPlot	If TRUE, the plots are not displayed on the current device. Default=FALSE. This is useful if one wants to only retrieve the object to insert the figure in a grid for instance.

Details

limits – This option allows generating t-SNE plots with equal color scale to compare the expression of different genes. By default, limits are the range of expression of a selected gene.

Value

A ggplot object of the gene expression colored tSNE.

Author(s)

Ilyess RACHEDI, based on code by Polina PAVLOVICH and Nicolas DESCOSTES.

See Also

retrieveTopClustersMarkers plotCellSimilarity plotCellHeatmap plotClusteredTSNE plotClustersSimilarity

Examples

## Object scr containing the results of previous steps
load(system.file("extdata/scrFull.Rdat", package="conclus"))

## t-SNE plot colored by expression of a  given gene.
plotGeneExpression(scr, getTopMarkers(scr)[1,1])

ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.