plotRegionCoverage: Makes plots for every region while summarizing the annotation

In leekgroup/derfinderPlot: Plotting functions for derfinder

Makes plots for every region while summarizing the annotation

Description

This function takes the regions found in calculatePvalues and assigns them genomic states contructed with makeGenomicState. The main workhorse functions are countOverlaps and findOverlaps. For an alternative plot check plotCluster which is much slower and we recommend it's use only after quickly checking the results with this function.

Usage

plotRegionCoverage(
  regions,
  regionCoverage,
  groupInfo,
  nearestAnnotation,
  annotatedRegions,
  txdb = NULL,
  whichRegions = seq_len(min(100, length(regions))),
  colors = NULL,
  scalefac = 32,
  ask = interactive(),
  ylab = "Coverage",
  verbose = TRUE
)

Arguments

regions	The ⁠$regions⁠ output from calculatePvalues.
regionCoverage	The output from getRegionCoverage used on regions.
groupInfo	A factor specifying the group membership of each sample. It will be used to color the samples by group.
nearestAnnotation	The output from matchGenes used on regions.
annotatedRegions	The output from annotateRegions used on regions.
txdb	A TxDb object. If specified, transcript annotation will be extracted from this object and used to plot the transcripts.
whichRegions	An integer vector with the index of the regions to plot.
colors	If NULL then brewer.pal with the 'Dark2' color scheme is used.
scalefac	The parameter used in preprocessCoverage.
ask	If TRUE then the user is prompted before each plot is made.
ylab	The name of the of the Y axis.
verbose	If TRUE basic status updates will be printed along the way.

Value

A plot for every region showing the coverage of each sample at each base of the region as well as the summarized annotation information.

Author(s)

Andrew Jaffe, Leonardo Collado-Torres

See Also

calculatePvalues, getRegionCoverage, matchGenes, annotateRegions, plotCluster

Examples

## Load data
library("derfinder")

## Annotate regions, first two regions only
regions <- genomeRegions$regions[1:2]
annotatedRegions <- annotateRegions(
    regions = regions,
    genomicState = genomicState$fullGenome, minoverlap = 1
)

## Find nearest annotation with bumphunter::matchGenes()
library("bumphunter")
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene)
nearestAnnotation <- matchGenes(x = regions, subject = genes)

## Obtain fullCov object
fullCov <- list("21" = genomeDataRaw$coverage)

## Assign chr lengths using hg19 information
library("GenomicRanges")
seqlengths(regions) <- seqlengths(getChromInfoFromUCSC("hg19",
    as.Seqinfo = TRUE
))[
    mapSeqlevels(names(seqlengths(regions)), "UCSC")
]

## Get the region coverage
regionCov <- getRegionCoverage(fullCov = fullCov, regions = regions)
#
## Make plots for the regions
plotRegionCoverage(
    regions = regions, regionCoverage = regionCov,
    groupInfo = genomeInfo$pop, nearestAnnotation = nearestAnnotation,
    annotatedRegions = annotatedRegions, whichRegions = 1:2
)

## Re-make plots with transcript information
plotRegionCoverage(
    regions = regions, regionCoverage = regionCov,
    groupInfo = genomeInfo$pop, nearestAnnotation = nearestAnnotation,
    annotatedRegions = annotatedRegions, whichRegions = 1:2,
    txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
)
## Not run: 
## If you prefer, you can save the plots to a pdf file
pdf("ders.pdf", h = 6, w = 9)
plotRegionCoverage(
    regions = regions, regionCoverage = regionCov,
    groupInfo = genomeInfo$pop, nearestAnnotation = nearestAnnotation,
    annotatedRegions = annotatedRegions, whichRegions = 1:2,
    txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, ask = FALSE
)
dev.off()

## End(Not run)

leekgroup/derfinderPlot documentation built on Dec. 17, 2024, 4:56 p.m.