Differentially expressed gene heatmap

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

plotDegHeatmap(object, ...)

# S4 method for class 'DESeqAnalysis'
plotDegHeatmap(
  object,
  i,
  contrastSamples = FALSE,
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL,
  ...
)

# S4 method for class 'DESeqResults'
plotDegHeatmap(
  object,
  DESeqTransform,
  direction = c("both", "up", "down"),
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL,
  title = TRUE,
  subtitle = TRUE,
  ...
)

Arguments

object

Object.

i

Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL.

For more information:

help(topic = "Extract", package = "base")

contrastSamples

logical(1). 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).

alphaThreshold

numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.

baseMeanThreshold

numeric(1) or NULL. Base mean (i.e. average expression across all samples) threshold. If left NULL, will use the cutoff defined in the object. Applies in general to DESeq2 RNA-seq differential expression output.

lfcThreshold

numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. If left NULL, will use the cutoff defined in the object.

...

Additional arguments.

DESeqTransform

DESeqTransform.

direction

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

title

logical(1), character(1). Include contrast name as title? Can manually define as character.

subtitle

logical(1). Include subtitle containing DEG information?

Value

Plot.

Details

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

Functions

• plotDegHeatmap(DESeqAnalysis): Passes to DESeqResults method.

• plotDegHeatmap(DESeqResults): Passes to plotHeatmap() SummarizedExperiment method defined in AcidPlots.

Note

Updated 2022-04-15.

Examples

data(deseq)

## DESeqAnalysis ====
plotDegHeatmap(deseq, i = 1L)
#> → Scaling matrix per row (z-score).
#> → Performing hierarchical clustering with `hclust()` method "ward.D2".