plotDEGHeatmap: Heatmap visualization of DEG result

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

Description

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.

Usage

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("MAST Result: ", useResult),
  ...
)

Arguments

inSCE	SingleCellExperiment inherited object. runMAST() has to be run in advance.
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 1.
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 "MAST Result: <useResult>".
...	Other arguments passed to plotSCEHeatmap

Value

A ComplexHeatmap::Heatmap object

Author(s)

Yichen Wang

Examples

data(scExample, package = "singleCellTK")
## Not run: 
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runDEAnalysis(inSCE = sce, method = "DESeq2",
                     groupName1 = "Sample1", groupName2 = "Sample2",
                     index1 = 1:100, index2 = 101:190,
                     analysisName = "DESeq2")
plotDEGHeatmap(sce, useResult = "DESeq2", fdrThreshold = 1, doLog = TRUE)

## End(Not run)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.