### R code from vignette source 'Vignette.Rnw' ################################################### ### code chunk number 1: setup ################################################### require(IdeoViz) require(RColorBrewer) ### nice colours data(binned_multiSeries) ################################################### ### code chunk number 2: example1 ################################################### ideo <- getIdeo("hg18") head(ideo) plotOnIdeo(chrom=seqlevels(binned_multiSeries), # which chrom to plot? ideoTable=ideo, # ideogram name values_GR=binned_multiSeries, # data goes here value_cols=colnames(mcols(binned_multiSeries)), # col to plot col=brewer.pal(n=5, 'Spectral'), # colours val_range=c(0,10), # set y-axis range ylab="array intensities", plot_title="Trendline example") ################################################### ### code chunk number 3: example2 ################################################### data(binned_singleSeries) data(hg18_ideo) # cytoBandIdeo table downloaded previously and stored as a data.frame. plotOnIdeo(chrom=seqlevels(binned_singleSeries), ideo=hg18_ideo, values_GR=binned_singleSeries, value_cols=colnames(mcols(binned_singleSeries)), plotType='rect', # plot as bars col='blue', vertical=T, val_range=c(-1,1), ylab="dummy score", plot_title="Discretized example") ################################################### ### code chunk number 4: example3 ################################################### data(binned_fullGenome) plotOnIdeo(chrom=seqlevels(binned_fullGenome), ideo=ideo, values_GR=binned_fullGenome, value_cols=colnames(mcols(binned_fullGenome)), plotType='rect', col='orange', addScale=F, # hide scale to remove visual clutter plot_title="Whole genome view", val_range=c(-1,1),cex.axis=0.5,chromName_cex=0.6) ################################################### ### code chunk number 5: example4 ################################################### ideo_hg19 <- getIdeo("hg19") chroms <- c("chr1","chr2","chrX") data(GSM733664_broadPeaks) head(GSM733664_broadPeaks) chrom_bins <- getBins(chroms, ideo_hg19,stepSize=5*100*1000) avg_peak <- avgByBin(data.frame(value=GSM733664_broadPeaks[,7]), GSM733664_broadPeaks[,1:3], chrom_bins) plotOnIdeo(chrom=seqlevels(chrom_bins), ideoTable=ideo_hg19, values_GR=avg_peak, value_cols='value', val_range=c(0,50), plotType='rect', col='blue', vertical=T ) ################################################### ### code chunk number 6: example5 ################################################### ideo_hg19 <- getIdeo("hg19") x <- GSM733664_broadPeaks gr <- GRanges(x[,1],IRanges(x[,2],x[,3])) pal <- brewer.pal(n=5,name="Dark2") chroms <- c("chr1","chr2","chrX") gr <- gr[which(seqnames(gr)%in% chroms)] chrom_bins <- getBins(chroms, ideo_hg19, stepSize=5*100*1000) grList <- list(gr,gr,gr,gr,gr) plotOnIdeo(chrom=seqlevels(chrom_bins), ideoTable=ideo_hg19, values_GR=grList, value_cols="value", plotType="seg_tracks", col=pal, vertical=F) ################################################### ### code chunk number 7: example6 ################################################### # assign group categories for (k in 1:5) { gp <- rep("type1",length(grList[[k]])); gp[(k*1000):((k*1000)+4000)] <- "type2" gp[1:1000] <- "type3" grList[[k]]$group <- gp print(table(grList[[k]]$group)) } # notice we don't name type3 - this is to show behaviour if a name is not specified namedCols <- c("orange","purple"); names(namedCols) <- c("type1","type2") plotOnIdeo(chrom=seqlevels(chrom_bins), ideoTable=ideo_hg19,values=grList, plotType="seg_tracks",col=namedCols,vertical=F) ################################################### ### code chunk number 8: Vignette.Rnw:137-138 ################################################### sessionInfo()