Heatmap visualization of DEG result
plotDEGHeatmap(
inSCE,
useResult,
onlyPos = FALSE,
log2fcThreshold = 0.25,
fdrThreshold = 0.05,
minGroup1MeanExp = NULL,
maxGroup2MeanExp = NULL,
minGroup1ExprPerc = NULL,
maxGroup2ExprPerc = NULL,
useAssay = NULL,
doLog = FALSE,
featureAnnotations = NULL,
cellAnnotations = NULL,
featureAnnotationColor = NULL,
cellAnnotationColor = NULL,
rowDataName = NULL,
colDataName = NULL,
colSplitBy = "condition",
rowSplitBy = "regulation",
rowLabel = S4Vectors::metadata(inSCE)$featureDisplay,
title = paste0("DE Analysis: ", useResult),
...
)
SingleCellExperiment inherited object.
character. A string specifying the analysisName
used when running a differential expression analysis function.
logical. Whether to only plot DEG with positive log2_FC
value. Default FALSE
.
numeric. Only plot DEGs with the absolute values of
log2FC larger than this value. Default 0.25
.
numeric. Only plot DEGs with FDR value smaller than this
value. Default 0.05
.
numeric. Only plot DEGs with mean expression in
group1 greater then this value. Default NULL
.
numeric. Only plot DEGs with mean expression in
group2 less then this value. Default NULL
.
numeric. Only plot DEGs expressed in greater then
this fraction of cells in group1. Default NULL
.
numeric. Only plot DEGs expressed in less then this
fraction of cells in group2. Default NULL
.
character. A string specifying an assay of expression value
to plot. By default the assay used for runMAST()
will be used.
Default NULL
.
Logical scalar. Whether to do log(assay + 1)
transformation on the assay used for the analysis. Default FALSE
.
data.frame
, with rownames
containing
all the features going to be plotted. Character columns should be factors.
Default NULL
.
data.frame
, with rownames
containing
all the cells going to be plotted. Character columns should be factors.
Default NULL
.
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
.
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
.
character. The column name(s) in rowData
that need
to be added to the annotation. Default NULL
.
character. The column name(s) in colData
that need
to be added to the annotation. Default NULL
.
character. Do semi-heatmap based on the grouping of
this(these) annotation(s). Should exist in either colDataName
or
names(cellAnnotations)
. Default "condition"
.
character. Do semi-heatmap based on the grouping of
this(these) annotation(s). Should exist in either rowDataName
or
names(featureAnnotations)
. Default "regulation"
.
FALSE
for not displaying; a variable in rowData
to display feature identifiers stored there; if have run
setSCTKDisplayRow
, display the specified feature name;
TRUE
for the rownames
of inSCE
; NULL
for
auto-display rownames
when the number of filtered feature is less
than 60. Default looks for setSCTKDisplayRow
information.
character. Main title of the heatmap. Default
"DE Analysis: <useResult>"
.
Other arguments passed to plotSCEHeatmap
A ggplot
object
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.
data("sceBatches")
logcounts(sceBatches) <- log1p(counts(sceBatches))
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")
#> Sat Mar 18 10:28:38 2023 ... Running DE with wilcox, Analysis name: w.aVSb
plotDEGHeatmap(sce.w, "w.aVSb")