Plot Differential Expression

Plot Differential Expression

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")
#> Warning: Zero sample variances detected, have been offset away from zero
#> Removing intercept from test coefficients
plotDiffEx(mouseBrainSubsetSCE, condition = "level1class",
            geneList = rownames(res)[1:50], annotationColors = "auto")