diagplot.de.heatmap: Diagnostic heatmap of differentially expressed genes

In pmoulos/metaseqr: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Description

This function plots a heatmap of the differentially expressed genes produced by the metaseqr workflow, useful for quality control, e.g. whether samples belonging to the same group cluster together.

Usage

    diagplot.de.heatmap(x, con = NULL, output = "x11",
        path = NULL, ...)

Arguments

x	the data matrix to create a heatmap for.
con	an optional string depicting a name (e.g. the contrast name) to appear in the title of the volcano plot.
output	one or more R plotting device to direct the plot result to. Supported mechanisms: "x11" (default), "png", "jpg", "bmp", "pdf", "ps".
path	the path to create output files.
...	further arguments to be passed to plot devices, such as parameter from par.

Value

The filenames of the plots produced in a named list with names the which.plot argument. If output="x11", no output filenames are produced.

Author(s)

Panagiotis Moulos

Examples

require(DESeq)
data.matrix <- counts(makeExampleCountDataSet())
sample.list <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
contrast <- "A_vs_B"
M <- normalize.edger(data.matrix,sample.list)
p <- stat.edger(M,sample.list,contrast)
diagplot.de.heatmap(data.matrix[p[[1]]<0.05,])

pmoulos/metaseqr documentation built on Dec. 29, 2020, 5:56 a.m.