Miscellaneous plotting
We have included a number of visualization routines in the jcvi package that might be useful to create customized plots.
Sometimes we wish to show categories for a number of chromosome regions in a genome. Let's say we want to plot the Arabidopsis genome. First, let's make a file that contains the chromosome sizes:
Chr1 30427671
Chr2 19698289
Chr3 23459830
Chr4 18585056
Chr5 26975502
This file can be created from the genome FASTA file and save it in athaliana.sizes. Now let's add a number of interesting features:
Chr1 1000000 3000000 type A
Chr4 12000000 15000000 type A
Chr2 5000000 10000000 type B
Chr5 20000000 22000000 type B
Chr2 15000000 18000000 LINE/SINE
Chr5 13000000 15000000 LINE/SINE
Chr3 2000000 3500000 LTR
This is known as the bed format, which must be tab-separated. Note that we use the functional class as the feature name. Since there are 4 classes, there will be 4 colors, one for each color. The command we use is:
python -m jcvi.graphics.chromosome features.bed \
--size=athaliana.sizes --title="*Arabidopsis* genome features" --gauge
What if we want to include centromeres? Append the following lines to features.bed:
Chr1 14511721 14538721 centromere
Chr2 3611838 3611883 centromere
Chr3 13589756 13589816 centromere
Chr4 3133663 3133674 centromere
Chr5 11194537 11194848 centromere
Run the above command again, now with features indicating where the centromeres are. We have the following output:
Some users may wish to change the labels or the colors of the features. In that case, use a .idmap file which is another tab-separated file for example athaliana.idmap:
LINE/SINE LS #377EB8
LTR LT #4DAF4A
type A TA #984EA3
type B TB #FF7F00
Column 2 is the legend label, while column 3 is the desired color. We then pass this file to the command line:
python -m jcvi.graphics.chromosome features.bed athaliana.idmap \
--size=athaliana.sizes --title="*Arabidopsis* genome features" --gauge