plotCumulPercentProfile: Plot the cumulative proportions obtained from...

In pgpmartin/GeneNeighborhood: Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

Description

Plot the cumulative proportions obtained from getCumulPercentProfiles

Usage

plotCumulPercentProfile(cumulprofs, gscolors = NULL, freeY = FALSE)

Arguments

cumulprofs	A data frame with cumulative percentage profiles for different gene sets. As produced by the getCumulPercentProfiles function.
gscolors	Optional named character vector with colors per gene sets
freeY	Logical (defaults to FALSE) indicating if y-axis scales for panels/facets should be different

Value

A ggplot object

Author(s)

Pascal GP Martin

See Also

getCumulPercentProfiles

#' @examples ## Get the TES of all genes: tes <- getTES(Genegr) ## Get their (presence/absence) coverage around (+/-50bp) genes (with 3 bins/gene): tescov <- annotationCoverageAroundFeatures(annot = tes, features = Genegr, sidedist = 50, usePercent = TRUE, nbins = 3) ## For each gene, find the closest TES and extend its presence to subsequent positions: extTEScov <- extendPointPresence(tescov, sidedist=50) ## Identify genes with a TES at less than 6bp from their TES, on any strand require(GenomicRanges) Dist2TES <- mcols(distanceToNearest(tes, ignore.strand = TRUE))$distance CloseTES <- names(Genegr)[Dist2TES<6] NotCloseTES <- names(Genegr)[Dist2TES>=6] #Also get the complementary set ## Calculate the cumulative percentage as the distance increases: CP <- getCumulPercentProfiles(extTEScov, list("All" = names(Genegr), "CloseTES" = CloseTES, "FarTES" = NotCloseTES)) ## Plot plotCumulPercentProfile(CP)

pgpmartin/GeneNeighborhood documentation built on Sept. 2, 2021, 6:37 a.m.