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 adenocarcinoma condition (data from TCGA). The heatmap ( as a second
dimension) display the logFC value(associated data) for each of the annotated gene. note that each chromosome location is a genomic
range that can contain many genes. So as a whole, you are viewing averaged data (logFc in this case) for all genes in a location.
But, wait, just hover over each location to see a single-strand of genes. These are actual genes with heatmap values according
to actual data.
On hovering over each chromosome you will see chromosome information. While, hover over each annotated location
to view the single-strand heatmap.
The Tooltip shows:
The heat color of the selected location.
The calculated values for the selected location like avg. , count, min. and max. value.
A single strand of genes in order in which they are mapped along with theit heat colors (depending on gene data value).
The genomic range of the selected location.
To know more about the plot (and tooltip information), see the package's vignette.