R/plotBrowserView.R

In mrkbrtkhn/cTagPipe:

plotBrowserView<-function(v,genRanges,winTx,gSelect=NULL,browserWindow) {
  gR <- makeGRangesFromDataFrame(do.call(rbind, lapply(v$data,
                                                       function(x) return(x$data[1, c(1:5)]))))
  gR$guide <- names(gR)
  gR
  mycol = rep(8L, length(v$data))
  if (!is.null(gSelect)) {
    mycol[which(names(v$data) %in% c(as.character(gSelect$V1),
                                     as.character(gSelect$V2)))] <- c(3, 4)
    print(mycol)
  }
  grTrack <- GeneRegionTrack(winTx, chromosome = as.character(seqnames(genRanges$stopWindow)),
                             start = start(genRanges$stopWindow) - browserWindow,
                             end = end(genRanges$stopWindow) + browserWindow, showId = TRUE,
                             geneSymbols = TRUE, name = "Gene Model", col.sampleNames = "black",
                             background.title = "white", col.axis = "black", col.title = "black",
                             col = "black", fill = "black", fontfamily = "Helvetica")
  annoTrack1 <- AnnotationTrack(gR, background.title = "white",
                                col.title = "black", name = "guideRNAs", featureAnnotation = "guide",
                                #fill = mycol
                                )
  axisTrack <- GenomeAxisTrack()
  plotTracks(list(grTrack, axisTrack, annoTrack1), chromosome = as.character(seqnames(genRanges$stopWindow)),
             from = start(genRanges$stopWindow) - browserWindow, to = end(genRanges$stopWindow) +
               browserWindow)
  }