Heatmap visualization of DEG result

plotDEGHeatmap(
  inSCE,
  useResult,
  doLog = FALSE,
  onlyPos = FALSE,
  log2fcThreshold = 0.25,
  fdrThreshold = 0.05,
  useAssay = NULL,
  featureAnnotations = NULL,
  cellAnnotations = NULL,
  featureAnnotationColor = NULL,
  cellAnnotationColor = NULL,
  rowDataName = NULL,
  colDataName = NULL,
  colSplitBy = "condition",
  rowSplitBy = "regulation",
  title = paste0("DE Analysis: ", useResult),
  ...
)

Arguments

inSCE: SingleCellExperiment inherited object.
useResult: character. A string specifying the analysisName used when running a differential expression analysis function.
doLog: Logical scalar. Whether to do log(assay + 1) transformation on the assay used for the analysis. Default FALSE.
onlyPos: logical. Whether to only plot DEG with positive log2_FC value. Default FALSE.
log2fcThreshold: numeric. Only plot DEGs with the absolute values of log2FC larger than this value. Default 0.25.
fdrThreshold: numeric. Only plot DEGs with FDR value smaller than this value. Default 0.05.
useAssay: character. A string specifying an assay of expression value to plot. By default the assay used for runMAST() will be used. Default NULL.
featureAnnotations: data.frame, with rownames containing all the features going to be plotted. Character columns should be factors. Default NULL.
cellAnnotations: data.frame, with rownames containing all the cells going to be plotted. Character columns should be factors. Default NULL.
featureAnnotationColor: A named list. Customized color settings for feature labeling. Should match the entries in the featureAnnotations or rowDataName. For each entry, there should be a list/vector of colors named with categories. Default NULL.
cellAnnotationColor: A named list. Customized color settings for cell labeling. Should match the entries in the cellAnnotations or colDataName. For each entry, there should be a list/vector of colors named with categories. Default NULL.
rowDataName: character. The column name(s) in rowData that need to be added to the annotation. Default NULL.
colDataName: character. The column name(s) in colData that need to be added to the annotation. Default NULL.
colSplitBy: character. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either colDataName or names(cellAnnotations). Default "condition".
rowSplitBy: character. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either rowDataName or names(featureAnnotations). Default "regulation".
title: character. Main title of the heatmap. Default "DE Analysis: <useResult>".
...: Other arguments passed to plotSCEHeatmap

Value

A ComplexHeatmap::Heatmap object

Details

A differential expression analysis function has to be run in advance so that information is stored in the metadata of the input SCE object. This function wraps plotSCEHeatmap. A feature annotation basing on the log2FC level called "regulation" will be automatically added. A cell annotation basing on the condition selection while running the analysis called "condition", and the annotations used from colData(inSCE) while setting the condition and covariates will also be added.

Author

Yichen Wang

Examples

data("sceBatches")
logcounts(sceBatches) <- log(counts(sceBatches) + 1)
sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'")
sce.w <- runWilcox(sce.w, class = "cell_type", classGroup1 = "alpha",
                   groupName1 = "w.alpha", groupName2 = "w.beta",
                   analysisName = "w.aVSb")
plotDEGHeatmap(sce.w, "w.aVSb")