inst/doc/Vignette.R

In IdeoViz: Plots data (continuous/discrete) along chromosomal ideogram

### R code from vignette source 'Vignette.Rnw'

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### code chunk number 1: setup
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require(IdeoViz)
require(RColorBrewer) ### nice colours
data(binned_multiSeries)


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### code chunk number 2: example1
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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")  


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### code chunk number 3: example2
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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")


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### code chunk number 4: example3
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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)


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### code chunk number 5: example4
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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
) 


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### code chunk number 6: example5
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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)


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### code chunk number 7: example6
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# 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)


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### code chunk number 8: Vignette.Rnw:137-138
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sessionInfo()