## ----setup, include = FALSE------------------------------------------------------------------------------------------- options(width=120) knitr::opts_chunk$set( collapse = TRUE, eval=interactive(), echo=TRUE, comment = "#>" ) ## ----eval=TRUE, echo=FALSE-------------------------------------------------------------------------------------------- knitr::include_graphics("igvR-basicDemo.png") ## ----loadLibraries, results='hide'----------------------------------------------------------------------------------- # library(igvR) ## ----createLoad, results='hide'--------------------------------------------------------------------------------------- # igv <- igvR() # setBrowserWindowTitle(igv, "simple igvR demo") # setGenome(igv, "hg38") ## ----genomes, echo=TRUE, results='asis'------------------------------------------------------------------------------- # print(getSupportedGenomes(igv)) ## ----initialDisplay, results='hide'---------------------------------------------------------------------------------- # showGenomicRegion(igv, "MYC") ## ----simple data.frame, results='hide'------------------------------------------------------------------------------- # loc <- getGenomicRegion(igv) # # tbl.bed <- data.frame(chrom=loc$chrom, start=loc$start + 2000, end=loc$end-2000, # name="simple.example", stringsAsFactors=FALSE) # # track <- DataFrameAnnotationTrack("simple bed", tbl.bed, color="random") # displayTrack(igv, track) ## ----bedgraph-like data.frame, results='hide'------------------------------------------------------------------------ # loc <- getGenomicRegion(igv) # size <- with(loc, 1 + end - start) # starts <- seq(loc$start, loc$end, by=5) # ends <- starts + 5 # values <- sample(1:100, size=length(starts), replace=TRUE) # # tbl.bedGraph <- data.frame(chrom=rep("chr8", length(starts)), start=starts, end=ends, # value=values, stringsAsFactors=FALSE) # # track <- DataFrameQuantitativeTrack("bedGraph", tbl.bedGraph, color="red", autoscale=FALSE, # min=80, max=100) # displayTrack(igv, track) # ## ----zoom out, results='hide'---------------------------------------------------------------------------------------- # loc <- getGenomicRegion(igv) # half.span <- round((loc$end-loc$start)/2) # # new.region <- with(loc, sprintf("%s:%d-%d", chrom, start-half.span, end+half.span)) # showGenomicRegion(igv, new.region) ## ----zoom out new, results='hide'------------------------------------------------------------------------------------ # # zoomOut(igv) # zoomIn(igv) ## ----sessionInfo------------------------------------------------------------------------------------------------------ # sessionInfo()