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Annotation chromosome plots created with chromoMap R package

Annotation chromosome plots created with chromoMap R package

by Lakshay Anand

Posted on May 18, 2018

chromoMap R visualization chromosome heatmap gene annotation annotation plot

A non interactive snapshot of 'annotation' type chromosome plot created using chromoMap

Hello guys, This post is just to show you a demo of how the interactive annotation plots, that was generated using chromoMap R package, looks like.

If you don't know about chromoMap , click here.

To know how to create 'annotation' plots by using chromoMap, see the vignette.

and now let's see how the plot looks like. (hover over the image to see the magic).

I annotated 630 genes that were predicted as differentially expressed (using R limma package)in pancreatic carcinoma condition (data from TCGA). The plot gives you an idea about the distribution of DE genes throughout the genome. I thought it would be nice if the plot can display additional information about these genes as another dimension. This is fulfilled by chromosome heatmaps. Check them out, if you havn't already.
On hovering over each chromosome you will see chromosome information. While, hover over each annotated location to view the annotated genes.
The Tooltip shows:

  • The genomic range for the selected location.
  • The total count of the genes annotated in the selected location.
  • Finally, the names of the genes annoted in the sequential order in which they are annoated in the selected location.

To know more about the plot (and tooltip information), see the package's vignette.

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Create chromosome heatmaps and annotate genes on chromosomes using chromoMap R package.

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