Graphics.Rnw
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\section*{An Introduction to Some Graphics in Bioconductor}
We first need to set up the basic data regarding the genome of interest. In this case we will look at human data and rely on information from Cheng Li.
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# hgByChroms: list matching affy names to location for each chorm (24) # hgCLengths: vector with length of 24 chromosomes data(hgByChroms) data(hgCLengths)
newChrom <- buildChromClass("Human", "Cheng Li's HG data", hgByChroms, hgCLengths) newChrom
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We have a number of different plotting features available to us.
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cPlot(newChrom) cPlot(newChrom,c("1","2"),fg="blue",scale="relative")
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par(mfrow=c(2,1)) for (sc in c("max","relative")) cPlot(newChrom,fg="blue",scale=sc)
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<< alongChrom >>=
data(eset) data(hgu95AProbLocs) cols <- c("red", "green", "blue") cols <- cols[eset$cov3]
par(mfrow=c(3,2)) alongChrom(eset, "1", newChrom, xloc="equispaced", plotFormat="cumulative", col=cols,lwd=2) alongChrom(eset, "1", newChrom, xloc="physical", col=cols,lwd=2) alongChrom(eset, "1", newChrom, xloc="equispaced", plotFormat="local", col=cols,lwd=2) alongChrom(eset, "1", newChrom, xloc="equispaced", plotFormat="local", col=cols, type="p", pch=16) alongChrom(eset, "1", newChrom, xlim = c(87511280,127717880), xloc="equispaced", plotFormat="local", col=cols, type="p", pch=16) alongChrom(eset, "1", newChrom, xloc="equispaced", plotFormat="image")
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