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.
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), ... )
inSCE | SingleCellExperiment inherited object.
|
---|---|
useResult | character. A string specifying the |
doLog | Logical scalar. Whether to do |
onlyPos | logical. Whether to only plot DEG with positive log2_FC
value. Default |
log2fcThreshold | numeric. Only plot DEGs with the absolute values of
log2FC larger than this value. Default |
fdrThreshold | numeric. Only plot DEGs with FDR value smaller than this
value. Default |
useAssay | character. A string specifying an assay of expression value
to plot. By default the assay used for |
featureAnnotations |
|
cellAnnotations |
|
featureAnnotationColor | A named list. Customized color settings for
feature labeling. Should match the entries in the |
cellAnnotationColor | A named list. Customized color settings for
cell labeling. Should match the entries in the |
rowDataName | character. The column name(s) in |
colDataName | character. The column name(s) in |
colSplitBy | character. Do semi-heatmap based on the grouping of
this(these) annotation(s). Should exist in either |
rowSplitBy | character. Do semi-heatmap based on the grouping of
this(these) annotation(s). Should exist in either |
title | character. Main title of the heatmap. Default
|
... | Other arguments passed to |
A ComplexHeatmap::Heatmap
object
Yichen Wang
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")