plotDEGHeatmap: Differentially expressed gene heatmap

Description Usage Arguments Details Examples

Description

This function is an extension of plotHeatmap() that is optimized for automatic handling differentially expressed genes, rather than requiring manual input of a gene vector. All of the optional parameters for plotHeatmap() are also supported by this function.

Usage

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## S4 method for signature 'DESeqResults'
plotDEGHeatmap(object, counts,
  direction = c("both", "up", "down"), scale = c("row", "column",
  "none"), clusteringMethod = "ward.D2", clusterRows = TRUE,
  clusterCols = TRUE, interestingGroups = NULL, showRownames = FALSE,
  showColnames = TRUE, treeheightRow = 50L, treeheightCol = 50L,
  color = viridis::viridis, legendColor = viridis::viridis,
  borderColor = NULL, title = NULL, ...)

## S4 method for signature 'DESeqAnalysis'
plotDEGHeatmap(object, results,
  contrastSamples = FALSE, direction = c("both", "up", "down"),
  scale = c("row", "column", "none"), clusteringMethod = "ward.D2",
  clusterRows = TRUE, clusterCols = TRUE, interestingGroups = NULL,
  showRownames = FALSE, showColnames = TRUE, treeheightRow = 50L,
  treeheightCol = 50L, color = viridis::viridis,
  legendColor = viridis::viridis, borderColor = NULL, title = NULL,
  ...)

Arguments

object

Object.

counts

DESeqTransform. Variance-stabilized counts suitable for heatmap. Object rownames must be identical to corresponding DESeqResults.

direction

character(1). Plot "both", "up", or "down" directions.

scale

character(1). Whether the values should be centered and scaled in either the row or column direction ("row", "column"), or remain unscaled ("none").

clusteringMethod

character(1). Clustering method. Accepts the same values as stats::hclust().

clusterRows

logical(1). Arrange with hierarchical clustering.

clusterCols

logical(1). Arrange with hierarchical clustering.

interestingGroups

character. Groups of interest that define the samples. If left unset, defaults to sampleName.

showRownames

logical(1). Show row or column names.

showColnames

logical(1). Show row or column names.

treeheightRow

integer(1). Size of the row and column dendrograms. Use 0 to disable.

treeheightCol

integer(1). Size of the row and column dendrograms. Use 0 to disable.

color

function, character, or NULL. Hexadecimal color function or values to use for plot.

We generally recommend these hexadecimal functions from the viridis package:

  • viridis::viridis() (default).

  • viridis::inferno().

  • viridis::magma().

  • viridis::plasma().

Alternatively, colors can be defined manually using hexadecimal values (e.g. c("#FF0000", "#0000FF")), but this is not generally recommended. Refer to the RColorBrewer package for hexadecimal color palettes that may be suitable. If set NULL, will use the default pheatmap colors.

legendColor

function or NULL. Hexadecimal color function to use for legend labels. Note that hexadecimal values are not supported. If set NULL, will use the default pheatmap colors.

borderColor

character(1) or NULL. Border color. Disabled by default for improved aesthetics.

title

character(1) or NULL. Plot title.

...

Additional arguments.

results

character(1) or integer(1). Name or position of DESeqResults.

contrastSamples

logical(1). Experimental. Only include the samples used to define the contrast passed to DESeq2::results(). This setting will break for complex DESeq2 contrasts (e.g. interaction effect).

Details

To adjust the annotation columns, modify the colData() of the counts argument, which must contain a SummarizedExperiment.

Examples

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data(deseq)

## DESeqAnalysis ====
plotDEGHeatmap(deseq, results = 1L)

steinbaugh/DESeqAnalysis documentation built on March 22, 2019, 5:51 p.m.