plotDEGHeatmap: Heatmap visualization of DEG result

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Heatmap visualization of DEG result

Description

Heatmap visualization of DEG result

Usage

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),
  ...
)

Arguments

inSCE	SingleCellExperiment inherited object.
useResult	character. A string specifying the analysisName used when running a differential expression analysis function.
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.
minGroup1MeanExp	numeric. Only plot DEGs with mean expression in group1 greater then this value. Default NULL.
maxGroup2MeanExp	numeric. Only plot DEGs with mean expression in group2 less then this value. Default NULL.
minGroup1ExprPerc	numeric. Only plot DEGs expressed in greater then this fraction of cells in group1. Default NULL.
maxGroup2ExprPerc	numeric. Only plot DEGs expressed in less then this fraction of cells in group2. Default NULL.
useAssay	character. A string specifying an assay of expression value to plot. By default the assay used for runMAST() will be used. Default NULL.
doLog	Logical scalar. Whether to do log(assay + 1) transformation on the assay used for the analysis. Default FALSE.
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".
rowLabel	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.
title	character. Main title of the heatmap. Default "DE Analysis: <useResult>".
...	Other arguments passed to plotSCEHeatmap

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.

Value

A ggplot object

Author(s)

Yichen Wang

Examples

data("sceBatches")
logcounts(sceBatches) <- log1p(counts(sceBatches))
sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'")
sce.w <- runWilcox(sce.w, class = "cell_type",
                   classGroup1 = "alpha", classGroup2 = "beta",
                   groupName1 = "w.alpha", groupName2 = "w.beta",
                   analysisName = "w.aVSb")
plotDEGHeatmap(sce.w, "w.aVSb")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.