degPlotWide: Plot selected genes on a wide format

Description Usage Arguments Value Examples

View source: R/clustering.R

Description

Plot selected genes on a wide format

Usage

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degPlotWide(counts, genes, group, metadata = NULL, batch = NULL)

Arguments

counts

DESeqDataSet object or expression matrix

genes

character genes to plot.

group

character, colname in colData to color points and add different lines for each level

metadata

data.frame, information for each sample. Not needed if DESeqDataSet given as counts.

batch

character, colname in colData to shape points, normally used by batch effect visualization

Value

ggplot showing the expresison of the genes on the x axis

Examples

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data(humanSexDEedgeR)
library(DESeq2)
idx <- c(1:10, 75:85)
dse <- DESeqDataSetFromMatrix(humanSexDEedgeR$counts[1:1000, idx],
humanSexDEedgeR$samples[idx,], design=~group)
dse <- DESeq(dse)
degPlotWide(dse, rownames(dse)[1:10], group="group")

Bioconductor-mirror/DEGreport documentation built on July 7, 2017, 10:53 p.m.