trackViewer Vignette: dandelionPlot

Abstract

Visualize high dense methylation or mutation data along with annotation as track layers via Dandelion Plot.

Dandelion Plot

Sometimes, there are as many as hundreds of SNPs invoved in one gene. Dandelion plot can be used to depict such dense SNPs. Please note that the height of the dandelion indicates the desity of the SNPs.

library(trackViewer)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
library(rtracklayer)
methy <- import(system.file("extdata", "methy.bed", package="trackViewer"), "BED")
gr <- GRanges("chr22", IRanges(50968014, 50970514, names="TYMP"))
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         org.Hs.eg.db,
                         gr=gr)
features <- c(range(trs[[1]]$dat), range(trs[[5]]$dat))
names(features) <- c(trs[[1]]$name, trs[[5]]$name)
features$fill <- c("lightblue", "mistyrose")
features$height <- c(.02, .04)
dandelion.plot(methy, features, ranges=gr, type="pin")