plotDegHeatmap: Differentially expressed gene heatmap

In acidgenomics/r-deseqanalysis: Acid Genomics DESeq2 Analysis Utilities

Differentially expressed gene heatmap

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

plotDegHeatmap(object, ...)

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

## S4 method for signature '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?

Details

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

Value

Plot.

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)

acidgenomics/r-deseqanalysis documentation built on March 30, 2024, 12:08 p.m.