plotTsne_cellProps: plotTsne_cellProps

In aertslab/AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

plotTsne_cellProps

Description

Plots the t-SNE coloured based on the known the cell properties

Usage

plotTsne_cellProps(
  tSNE,
  cellInfo,
  colVars = NULL,
  cex = 1,
  sub = "",
  gradientCols = c("yellow", "orange", "red"),
  showLegend = TRUE
)

Arguments

tSNE	t-SNE coordinates (e.g. tSNE$Y)
cellInfo	Dataframe with cell phenodata
colVars	Colors for the cell properties (optional)
cex	Scaling factor for the dots in the scatterplot
sub	Subtitle (e.g. tSNE type)
gradientCols	Gradient colors for numerical variables
showLegend	Whether to show the legend

Value

Plots the t-SNE

Examples

######
# Fake run of AUCell
set.seed(123)
exprMatrix <- matrix(
  data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
  nrow=20, 
  dimnames=list(paste("Gene", 1:20, sep=""), 
                paste("Cell", 1:500, sep="")))
geneSets <- list(geneSet1=sample(rownames(exprMatrix), 10),
                 geneSet2=sample(rownames(exprMatrix), 5))

cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats = FALSE)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1)
selectedThresholds <- rowMeans(getAUC(cells_AUC))
cellsTsne<- Rtsne::Rtsne(t(exprMatrix),max_iter = 10)$Y
# cellsTsne<- tsne::tsne(t(exprMatrix),max_iter = 10)
rownames(cellsTsne) <- colnames(exprMatrix)
######


par(mfrow=c(2,3))
thrs <- AUCell_plotTSNE(tSNE=cellsTsne, exprMat=NULL,
                        cellsAUC=cells_AUC, thresholds=selectedThresholds, 
                        plots = c("histogram", "binaryAUC", "AUC"))
 


#####
# Color based on the known phenodata:
cellInfo <- data.frame(cellType1=sample(LETTERS[1:3],ncol(exprMatrix), replace=TRUE), 
                       cellType2=sample(letters[5:7],ncol(exprMatrix), replace=TRUE), 
                       nGenes=abs(rnorm(ncol(exprMatrix))), 
                       row.names=colnames(exprMatrix))
colVars <- list(cellType2=setNames(c("skyblue","magenta", "darkorange"),letters[5:7]))
# dev.off()
plotTsne_cellProps(cellsTsne, cellInfo, colVars=colVars)

aertslab/AUCell documentation built on March 12, 2024, 11:40 p.m.