plotDEGHeatmap {singleCellTK} | R Documentation

## Heatmap visualization of DEG result

### 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)

[Package singleCellTK version 2.0.0 Index]