plotGetCounts: Given the output from getCounts, plot a density plot of log2...

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

Description

Given the output from getCounts, plot a density plot of log2 RPKM values of regulation regions

Usage

plotGetCounts(countsConsPeaks, viewer = TRUE, palette = "Set1",
  xlabel = "Log2 Normalized Read Counts", ylabel = "Density",
  xlabelsize = "15px", ylabelsize = "15px",
  maintitle = "Density of log2 read counts\n(normalized by library and region sizes)",
  maintitlesize = "20px")

Arguments

countsConsPeaks	output generated from getCounts
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
xlabel	label for x-axis (default, "log2 normalized read counts")
ylabel	label for y-axis (default, "Density")
xlabelsize	size of xlabel (default, 15px)
ylabelsize	size of ylabel (default, 15px)
maintitle	main title (default, "Density of log2 read counts (normalized by library and region sizes)")
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,
                                 sampleinfo = csvfile,
                                 reference = 'SAEC',
                                 chrom = 'chr21')
plotGetCounts(consensusPeaksCounts)
## End(Not run)

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