TME_plot: TME_plot

In miccec/scTHI: Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data

TME_plot

Description

Generates a plot on the t-SNE coordinates, labeling cells by TME classification.

Usage

TME_plot(tsneData, Class, cexPoint = 0.8)

Arguments

tsneData	X and y coordinates of points in the plot.
Class	Object returned by TME_classification function.
cexPoint	Set the point size.

Value

None

Examples

library(scTHI.data)
data(scExample)
result <-  scTHI_score(scExample,
           cellCusterA = colnames(scExample)[1:30],
           cellCusterB = colnames(scExample)[31:100],
           cellCusterAName = "ClusterA",
           cellCusterBName = "ClusterB", filterCutoff = 0,
           pvalueCutoff = 1, nPermu = 100, ncore = 8)
result <- scTHI_runTsne(result)
Class <- TME_classification(scExample)
TME_plot(tsneData = result$tsneData, Class)

miccec/scTHI documentation built on April 21, 2023, 12:40 p.m.