plotDEGPCA: Plot DEG PCA

In WeiSong-bio/roryk-bcbioRNASeq: RNA-Seq Utilities

Description

Plot DEG PCA

Usage

plotDEGPCA(results, counts, ...)

## S4 method for signature 'DESeqResults,SummarizedExperiment'
plotDEGPCA(results, counts,
  interestingGroups, alpha, lfcThreshold = 0L, color = scale_color_hue(),
  label = FALSE, title = "deg pca", return = c("ggplot", "data.frame"))

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

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

Arguments

results	DESeqResults object.
counts	Object containing a normalized counts matrix.
...	Additional arguments.
interestingGroups	Character vector denoting groups of interest that define the samples. If left unset, defaults to sampleName.
alpha	Adjusted P value ("alpha") cutoff.
lfcThreshold	Log fold change ratio (base 2) cutoff threshold.
color	Desired ggplot color scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().
label	Superimpose sample text labels on the plot.
title	Title of plot.
return	Object class to return. Uses match.arg() internally and picks the first item in the vector by default.
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.

Value

ggplot or data.frame.

Author(s)

Michael Steinbaugh

See Also

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

Examples

# DESeqResults, SummarizedExperiment ====
plotDEGPCA(
    results = res_small,
    counts = rld_small,
    label = TRUE
)

# DESeqResults, bcbioRNASeq ====
plotDEGPCA(
    results = res_small,
    counts = bcb_small,
    label = TRUE
)

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