plotCountAnalysis: Create a volcano plot from the output of categAltrePeaks

In Mathelab/ALTRE: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

Create a volcano plot from the output of categAltrePeaks

Usage

plotCountAnalysis(altrepeakscateg, viewer = TRUE, palette = c("#C71585",
  "#d3d3d3", "#00E5EE", "#000080"), maintitlelefty = "TSS-distal",
  maintitlerighty = "TSS-proximal", ylabel = "-log10 pvalue",
  xlabel = "log2fold change", xlabelsize = "15px", ylabelsize = "15px",
  maintitlesize = "20px")

Arguments

altrepeakscateg	output generated from countanalysis() then categAltrePeaks()
viewer	whether the plot should be displayed in the RStudio viewer or in Shiny/Knittr
palette	choose an RColorBrewer palette ("Set1", "Set2", "Set3", "Pastel1", "Pastel2", "Paired", etc.) or submit a vector of colors
maintitlelefty	main title (default, "TSS-distal")
maintitlerighty	main title (default, "TSS-proximal")
ylabel	label for y-axis (default, "Density")
xlabel	label for x-axis (default, "-log10 pvalue")
xlabelsize	size of xlabel (default, 15px)
ylabelsize	size of ylabel (default, 15px)
maintitlesize	main title size (default, 20px)

Value

a highcharter object

Examples

## Not run: 
csvfile <- loadCSVFile("DNaseEncodeExample.csv")
samplePeaks <- loadBedFiles(csvfile)
consensusPeaks <- getConsensusPeaks(samplepeaks = samplePeaks, minreps = 2)
TSSannot <- getTSS()
consensusPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consensusPeaks,
                                          TSS = TSSannot,
                                          merge = TRUE,
                                          regionspecific = TRUE,
                                          distancefromTSSdist = 1500,
                                          distancefromTSSprox = 1000)
consensusPeaksCounts <- getCounts(annotpeaks = consensusPeaksAnnotated,
                              reference = 'SAEC',
                              sampleinfo = csvfile,
                              chrom = 'chr21')
alteredPeaks <- countanalysis(counts=consensusPeaksCounts,
                             pval=0.01,
                             lfcvalue=1)
alteredPeaksCategorized <- categAltrePeaks(alteredPeaks,
                             lfctypespecific = 1.5,
                             lfcshared = 1.2,
                             pvaltypespecific = 0.01,
                             pvalshared = 0.05)
plotCountAnalysis(altrepeakscateg = alteredPeaksCategorized)

## End(Not run)

Mathelab/ALTRE documentation built on May 7, 2019, 3:41 p.m.