diagplotDeHeatmap: Diagnostic heatmap of differentially expressed genes

Description Usage Arguments Value Author(s) Examples

View source: R/plot.R

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

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    diagplotDeHeatmap(x, scale = c("asis", "zscore"), con = NULL, 
        output = "x11", path = NULL, ...)

Arguments

x

the data matrix to create a heatmap for.

scale

value scale in the heatmap. As provided (scale="asis", default) or Z-scores (scale="zscore")

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 whichPlot argument. If output="x11", no output filenames are produced.

Author(s)

Panagiotis Moulos

Examples

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dataMatrix <- metaseqR2:::exampleCountData(2000)
sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
contrast <- "A_vs_B"
M <- normalizeEdger(dataMatrix,sampleList)
p <- statEdger(M,sampleList,contrast)
diagplotDeHeatmap(dataMatrix[p[[1]]<0.05,])

metaseqR2 documentation built on Nov. 8, 2020, 7:34 p.m.