plotAbundanceBar {PloGO2}

R Documentation

Function to plot abundance barplot

Description

Plot the aggregated abundance barplot for all files/clusters

Usage

plotAbundanceBar(mat.abundance, mat.counts, min.count=5)

Arguments

mat.abundance	A matrix of abundance
mat.counts	A matrix of the counts
min.count	The cutoff for the minimum counts to be included

Value

None returned, generate a barplot.

Author(s)

J.Wu

Examples

path <- system.file("files", package = "PloGO2")
# run PloPathway with list of id's, data file and reference
res <- PloPathway( zipFile=paste(path, "PWFiles.zip", sep="/"), 
	reference="Alldata", 
	data.file.name = paste(path, "Abundance_data.csv", sep="/"),
	datafile.ignore.cols = 1)
	
png("AbundanceBarplot.png", 2500, 2000, res=300)
par(mar=c(4,10,4,14))

plot.res <- plotAbundanceBar(res$aggregatedAbundance, res$Counts)

dev.off()

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