plotDiffEx: Plot Differential Expression

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

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")

mmkhan19/singleCellTK documentation built on March 22, 2022, 7:43 a.m.