plotCombineAnnotatePeaks: Given the output from combineAnnotatePeaks, plot a barplot...

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

Description

Given the output from combineAnnotatePeaks, plot a barplot showing number of peaks before/after merging or length of peaks before/after merging (only works if peaks were merged)

Usage

plotCombineAnnotatePeaks(conspeaks, viewer = TRUE, palette = "Set1",
  rightmaintitle = "Mean Length of REs", leftmaintitle = "Number of REs",
  xlabels = c("Before merging", "After merging"),
  leftylabel = "Number of REs", rightylabel = "Mean Length of REs",
  xlabelsize = "15px", leftylabelsize = "15px", rightylabelsize = "15px",
  leftmaintitlesize = "20px", rightmaintitlesize = "20px")

Arguments

conspeaks	output generated from combineAnnotatePeaks
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
rightmaintitle	main title for mean length of REs plot (default, "Mean length of REs")
leftmaintitle	main title for number of REs plot (default, "Number of REs")
xlabels	labels for x-axis (default, Before merging/After merging)
leftylabel	label for y-axis for number of REs plot (default, "Number of REs")
rightylabel	label for y-axis for mean length plot (default, "Mean length of REs")
xlabelsize	size of xlabel (default, 15px)
leftylabelsize	size of leftylabel (default, 15px)
rightylabelsize	size of rightylabel (default, 15px)
leftmaintitlesize	main title size for number of REs plot (default, 20px)
rightmaintitlesize	main title size for mean length of REs plot (default 15px)

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)
plotCombineAnnotatePeaks(consensusPeaksAnnotated)

## End(Not run)

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