Sunday, February 20, 2011

Qiime (3) Heatmap



This example should really be part of the previous post (here), about the first segment of the overview tutorial for Qiime (here). One script in Qiime makes a heatmap, and it is quite something. To do this example, I modified #7 from last time to save otu_table.txt in a sub-directory rather than write to the screen. The second command makes the heat map.

Here are the commands:


make_otu_table.py -i otus/seqs_otus.txt -t tax/reps_tax_assignments.txt -o figs/otu_table.txt

make_otu_heatmap_html.py -i figs/otu_table.txt -o figs


The first thing is that the output is html and can be displayed in the browser (great idea). The second is that it's quite complicated, with more than 5000 lines of javascript required for display. It allows drag and drop of the table rows, and custom mapping files to control the sorted order of the table rows. There are "tool tips" to display detail for each cell.

The primary author, Jesse Stombaugh, and also the library authors Erik Bosrup (overLIB) and John Resig (jQuery) obviously put a huge amount of effort into this.

I am not sure why the default output from this example (by Taxonomy) looks so weird. Anybody know why there are so many duplicate row names?

I would probably make the red used for the highest counts a brighter color.

Put this on the list for more investigation.


1 comment:

jO said...

Why there is rows with the exactly the same name is because the resolution of the taxonomy inhibits further assignment (e.g. to genus or species level). Even if the rows are exactly the same, they still represent different OTUs.