## ----echo=FALSE, results="hide", warning=FALSE-------------------------------- suppressPackageStartupMessages({ library(trackViewer) library(rtracklayer) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) library(VariantAnnotation) library(httr) }) knitr::opts_chunk$set(warning=FALSE, message=FALSE) ## ----fig.width=4.5,fig.height=3----------------------------------------------- library(trackViewer) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) library(rtracklayer) methy <- import(system.file("extdata", "methy.bed", package="trackViewer"), "BED") gr <- GRanges("chr22", IRanges(50968014, 50970514, names="TYMP")) trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, gr=gr) features <- c(range(trs[[1]]$dat), range(trs[[5]]$dat)) names(features) <- c(trs[[1]]$name, trs[[5]]$name) features$fill <- c("lightblue", "mistyrose") features$height <- c(.02, .04) dandelion.plot(methy, features, ranges=gr, type="pin") ## ----fig.width=4.5,fig.height=3----------------------------------------------- methy$color <- 3 methy$border <- "gray" ## Score info is required and the score must be a number in [0, 1] m <- max(methy$score) methy$score <- methy$score/m dandelion.plot(methy, features, ranges=gr, type="fan") ## ----fig.width=4.5,fig.height=4----------------------------------------------- methy$color <- rep(list(c(3, 5)), length(methy)) methy$score2 <- (max(methy$score) - methy$score)/m legends <- list(list(labels=c("s1", "s2"), fill=c(3, 5))) dandelion.plot(methy, features, ranges=gr, type="pie", legend=legends) ## ----fig.width=4.5,fig.height=3.5--------------------------------------------- ## Less dandelions dandelion.plot(methy, features, ranges=gr, type="circle", maxgaps=1/10) ## ----fig.width=4.5,fig.height=4----------------------------------------------- ## More dandelions dandelion.plot(methy, features, ranges=gr, type="circle", maxgaps=1/100) ## ----fig.width=4,fig.height=4------------------------------------------------- maxgaps <- tile(gr, n = 10)[[1]] dandelion.plot(methy, features, ranges=gr, type="circle", maxgaps=maxgaps) ## ----fig.width=4.5,fig.height=3----------------------------------------------- dandelion.plot(methy, features, ranges=gr, type="pie", maxgaps=1/100, yaxis = TRUE, heightMethod = mean, ylab='mean of methy scores') ## ----fig.width=4.5,fig.height=3----------------------------------------------- yaxis = c(0, 0.5, 1) dandelion.plot(methy, features, ranges=gr, type="pie", maxgaps=1/100, yaxis = yaxis, heightMethod = mean, ylab='mean of methy scores') ## ----sessionInfo, results='asis'---------------------------------------------- sessionInfo()