Plot an ideogram

The first step when creating a karyoplot is to create the empty ideogram plot where data will later be added.

The plotKaryotype function does just that and returns the karyoplot object. We will need this object later on when we need to add data to the plot.

By default it will create a karyoplot of the human genome hg19


kp <- plotKaryotype()

plot of chunk Figure1

It is possible to specify other genomes. If it’s one of the few included in the package it will be plotted from cache and if it’s not, karyoploteR will try to load the corresponding BSGenome library and connect to UCSC to download the the cytobands. The BSGenome needs to be installed in the system. Use installed.genomes() from package BSGenome to list them.

kp <- plotKaryotype(genome = "dm6")

plot of chunk Figure2