plotDEGHeatmap: Differentially Expressed Gene Heatmap

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

This function is a simplified version of plotHeatmap() that is optimized for handling a DESeqResults object rather a gene vector. All of the optional parameters for plotHeatmap() are also available to this function.

Usage

plotDEGHeatmap(results, counts, ...)

## S4 method for signature 'DESeqResults,SummarizedExperiment'
plotDEGHeatmap(results, counts,
  alpha, lfcThreshold = 0L, title = TRUE, ...)

## S4 method for signature 'DESeqResults,DESeqDataSet'
plotDEGHeatmap(results, counts, ...)

## S4 method for signature 'DESeqResults,bcbioRNASeq'
plotDEGHeatmap(results, counts,
  normalized = c("rlog", "vst", "tmm", "tpm"), ...)

Arguments

results	DESeqResults object.
counts	Object containing a normalized counts matrix.
...	Passthrough arguments to plotHeatmap().
alpha	Adjusted P value ("alpha") cutoff.
lfcThreshold	Log fold change ratio (base 2) cutoff threshold.
title	Optional. Plot title.
normalized	Character indicating which normalization method to apply: "tpm": Transcripts per million (tximport). "tmm": edgeR trimmed mean of M-values. Calculated on the fly. "rlog": DESeq2 log2 regularized log transformation. "vst": DESeq2 log2 variance stabilizing transformation.

Details

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

Value

Show heatmap and invisibly return a list of the components.

Author(s)

Michael Steinbaugh

See Also

• help("plotHeatmap", "bcbioBase").

• findMethod("plotHeatmap", "SummarizedExperiment").

Other Differential Expression Functions: alphaSummary, contrastName, plotDEGPCA, plotMeanAverage, plotVolcano, resultsTables

Examples

# DESeqResults, SummarizedExperiment ====
plotDEGHeatmap(
    results = res_small,
    counts = rld_small
)

# DESeqResults, DESeqDataSet ====
# This always uses normalized counts
# Using default ggplot2 colors
plotDEGHeatmap(
    results = res_small,
    counts = dds_small,
    color = NULL,
    legendColor = NULL
)

# DESeqResults, bcbioRNASeq ====
plotDEGHeatmap(
    results = res_small,
    counts = bcb_small
)

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.