plotConsensusPeaks: Given the output from getConsensusPeaks, generate a barplot...

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

Description

Given the output from getConsensusPeaks, generate a barplot of countstatistics

Usage

plotConsensusPeaks(samplepeaks, viewer = TRUE, palette = "Set1",
  xlabel = NULL, ylabel = "Peak Counts", xlabelsize = "15px",
  ylabelsize = "15px", maintitle = "Peak Counts by Cell Type",
  subtitle = "For bioreplicates and their merged consensus track",
  maintitlesize = "20px", subtitlesize = "15px")

Arguments

samplepeaks	output generated from getConsensusPeaks
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, types of peaks - e.g. ConsensusPeaks, rep1, rep2, etc.)
ylabel	label for y-axis (default, "Peak Counts")
xlabelsize	size of xlabel (default, 15px)
ylabelsize	size of ylabel (default, 15px)
maintitle	main title (default, "Peak Counts by Cell Type")
subtitle	subtitle (default, "For bioreplicates and their merged consensus track")
maintitlesize	main title size (default, 20px)
subtitlesize	subitle size (default 15px)

Value

a highcharter object

Examples

## Not run: 
csvfile <- loadCSVFile("DNaseEncodeExample.csv")
samplePeaks <- loadBedFiles(csvfile)
consensusPeaks <- getConsensusPeaks(samplepeaks = samplePeaks,
minreps = 2)
plotConsensusPeaks(samplepeaks = consensusPeaks)
## End(Not run)

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