Plot all the significant GOterms from custom association file

[rafarios50]

I have a custom annotation from a non model organism and want to plot the graph of the significant GOterms found.

The idea is to be able to plot the graph similar to the one shown in the this notebook: https://github.com/tanghaibao/goatools/blob/master/notebooks/goea_nbt3102.ipynb

But im not sure how to load my custom association file to create the GOEA object.

Also, couldnt find the example files to run the notebook, to replicate it and try to match those files from my data.

Could you please help me explaining me how to do that, or where to find the example files?

Thanks,

[algogalo]

Hi there @rafarios50 ,

You need to import and use the IdToGosReader method to read an association file from a custom database of a non-model organism.

Basically you need to make sure that your association file is in the same shape and format as the example provided here.

Then, in step "2b. Load Associations" of the notebook you mentioned, you create the objanno object using IdToGosReader function. You have to specify two parameters for that function: the path to your association file and the GODag that was previously downloaded in step "2a. Load Ontologies" of that same notebook.

Here is how the code looks like

from __future__ import print_function
from goatools.anno.idtogos_reader import IdToGosReader
objanno=IdToGosReader("association.txt",godag=obodag)

Good luck and I hope this is still useful almost three years later :D