plotCompareMethods: Plots a pie that compares altered regions as determined by...

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

Description

Plots a pie that compares altered regions as determined by peak presence or by #' differential counts. The type of regulatory region (TSS-proximal, TSS-distal, or both) and type of peak comparison (intensity or peak) must be specified.

Usage

plotCompareMethods(analysisresultsmatrix, viewer = TRUE, region = "both",
  method = "Intensity", palette = c("#C71585", "#d3d3d3", "#00E5EE",
  "#000080"), maintitle = NULL, maintitlesize = "16px")

Arguments

analysisresultsmatrix	analysisresults of Intensity analysis place into analysisresults matrix by the analyzeanalysisresults function
viewer	whether the plot should be displayed in the RStudio viewer or in Shiny/Knittr
region	pick a region, regions can be 'TSS-distal', 'TSS-proximal', or 'both' – INCLUDE quotes
method	pick a method, methods can be 'Intensity' or 'Peak' include quotes
palette	choose an RColorBrewer palette ("Set1", "Set2", "Set3", "Pastel1", "Pastel2", "Paired", etc.) or submit a vector of colors
maintitle	main title (default generated from sample names)
maintitlesize	main title size (default, 20px)

Value

pie chart

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')
alteredPeaks <- countanalysis(counts = consensusPeaksCounts,
pval = 0.01,
lfcvalue = 1)
alteredPeaksCategorized <- categAltrePeaks(alteredPeaks,
                                          lfctypespecific = 1.5,
                                          lfcshared = 1.2,
                                          pvaltypespecific = 0.01,
                                          pvalshared = 0.05)
comparePeaksAnalysisResults <- comparePeaksAltre(alteredPeaksCategorized)
plotCompareMethods(analysisresultsmatrix = comparePeaksAnalysisResults)

## End(Not run)

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