basicIntro.R
In igvR: igvR: integrative genomics viewer

## ----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)

## ----sessionInfo------------------------------------------------------------------------------------------------------
#  sessionInfo()