scTHI_plotPairs: scTHI_plotPairs

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

Description

Generates a plot on the t-SNE coordinates to show the expression levels of an interaction pair of interest. Each cell is colored according to the corresponding gene expression value.

Usage

scTHI_plotPairs(scTHIresult, cexPoint = 0.8, interactionToplot)

Arguments

scTHIresult	scTHI object.
cexPoint	Set the point size.
interactionToplot	Interaction pair to plot.

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)
scTHI_plotPairs(result,interactionToplot = "CXCL12_CD4")

scTHI documentation built on Nov. 8, 2020, 7:37 p.m.