trackViewer Vignette: lollipopPlot

Abstract

Visualize methylation or mutation sites along with annotation as track layers.

Lolliplot

Lolliplot is for the visualization of the methylation/variant/mutation data.

library(trackViewer)
SNP <- c(10, 12, 1400, 1402)
sample.gr <- GRanges("chr1", IRanges(SNP, width=1, names=paste0("snp", SNP)))
features <- GRanges("chr1", IRanges(c(1, 501, 1001), 
                                    width=c(120, 400, 405),
                                    names=paste0("block", 1:3)))
lolliplot(sample.gr, features)

## More SNPs
SNP <- c(10, 100, 105, 108, 400, 410, 420, 600, 700, 805, 840, 1400, 1402)
sample.gr <- GRanges("chr1", IRanges(SNP, width=1, names=paste0("snp", SNP)))
lolliplot(sample.gr, features)

## Define the range
lolliplot(sample.gr, features, ranges = GRanges("chr1", IRanges(104, 109)))

Change the lolliplot color

Change the color of the features.

features$fill <- c("#FF8833", "#51C6E6", "#DFA32D")
lolliplot(sample.gr, features)