plotDEGHeatmap: Differentially Expressed Gene Heatmap

Description Usage Arguments Details Value Author(s) See Also Examples

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
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

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
# 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
)

WeiSong-bio/roryk-bcbioRNASeq documentation built on July 6, 2019, 12:02 a.m.