resizeGenes: 'resizeGenes' resize select subsets of genes plotted from a...

In harrig12/pointszr: Point Resizing for Volcano Plots

Description

resizeGenes plot the differentially expressed genes, as specified
in DDSresult, sized accordingly

Usage

resizeGenes(DDSresult, geneLists, sz = lseq(1, 6, length.out =
  length(geneLists)), pch = 20, ...)

Arguments

DDSresult	a DESeqResults object
geneLists	a list of lists of genes to be resized
sz	a list of sized to be assigned to genes.
pch	point style to be displayed. by default pch = 20.
...	additional arguments to pass to par.

Value

no return, plotting side effect

See Also

par, overlay, , vplot

Examples

require(DESeq2)
simDDS <- DESeq(simDDS)
res <- results(simDDS)
vplot(res, xlab = "log2FoldChange", ylab = "-log10(pvalue)")
potentialCancerDrivers <- sample(rownames(res), 100)
knownOncogenes <- c("gene866", "gene882", "gen614", "gene89", "gene70", "gene700", "gene205")
knownTumorRepressors <- c("gene614", "gene170", "gene441", "gene229", "gene363")
geneSets <- list(potentialCancerDrivers, knownOncogenes, knownTumorRepressors)
resizeGenes(res, geneSets, sz = 1:3, col = 2)
legend("top",c("Known Occogenes","Known Tumor Repressors",
               "Potential Cancer drivers", "Other Genes"),
       pt.cex = 1:3, col = c(2,2,2,1), pch = 20)

harrig12/pointszr documentation built on April 10, 2020, 10:45 p.m.