plotTsne_cellProps {AUCell} | R Documentation

## 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)

[Package AUCell version 1.14.0 Index]