plotDiffEx {singleCellTK} | R Documentation

## Plot Differential Expression

### Description

Plot Differential Expression

### Usage

    plotDiffEx(inSCE, useAssay = "logcounts", condition, geneList,
      clusterRow = TRUE, clusterCol = TRUE, displayRowLabels = TRUE,
      displayColumnLabels = TRUE, displayRowDendrograms = TRUE,
      displayColumnDendrograms = TRUE, annotationColors = NULL,
      scaleExpression = TRUE, columnTitle = "Differential Expression")

### Arguments

`inSCE` | Input data object that contains the data to be plotted. Required
`useAssay` | Indicate which assay to use. Default is "logcounts"
`condition` | The condition used for plotting the heatmap. Required
`geneList` | The list of genes to put in the heatmap. Required
`clusterRow` | Cluster the rows. The default is TRUE
`clusterCol` | Cluster the columns. The default is TRUE
`displayRowLabels` | Display the row labels on the heatmap. The default is TRUE.
`displayColumnLabels` | Display the column labels on the heatmap. The default is TRUE
`displayRowDendrograms` | Display the row dendrograms on the heatmap. The default is TRUE
`displayColumnDendrograms` | Display the column dendrograms on the heatmap. The default is TRUE.
`annotationColors` | Set of annotation colors for color bar. If null, no color bar is shown. default is NULL.
`scaleExpression` | Row scale the heatmap values. The default is TRUE.
`columnTitle` | Title to be displayed at top of heatmap.

### Value

ComplexHeatmap object for the provided geneList annotated with the condition.

### Examples

    data("mouseBrainSubsetSCE")
    res <- scDiffEx(mouseBrainSubsetSCE,
                    useAssay = "logcounts",
                    "level1class",
                    diffexmethod = "limma")
    plotDiffEx(mouseBrainSubsetSCE, condition = "level1class",
                geneList = rownames(res)[1:50], annotationColors = "auto")

[Package singleCellTK version 1.7.0 Index]