makeGO

Plot Fold Enrichment (FE) from the PantherDB (http://go.pantherdb.org) GO (Gene Ontology) output into a Bubble Plot (saved as a high dpi .pdf file).

Installation Guide:

Install from Github

git clone https://github.com/Lucas-Servi/makeGO.git
cd makeGO

• sudo, if required

System Requirements

Hardware requirements

makeGO package requires only a standard computer with enough RAM to support the in-memory operations.

Software requirements

OS Requirements

The package has been tested on the following systems:

• Linux: Ubuntu 18.04+

Python Dependencies

makeGO depends on:

matplotlib
numpy
pandas
seaborn

Any of this libraries can be installed by using pip install <library name>

How to use

This script runs on terminal with the following parameters:

python3 GO_plot.py -i <input-file.txt> <input-file.txt> <input-file.txt> -names <name1> <name2> <name3> -o <output-file.pdf>

• -i | --input-file: files(.txt) from PantherDB, each file correspond to a set or cluster. Same GO analysis (Biological processes, Cellular Components, etc.) are recomemended. Full directory must be used (e.g.: /home/.../file1.txt)
• -o | --output-file: a .pdf format file containing the dot plot where y-axis show GO groups and x-axis are the differente sets/clusters from the input-files.
• -names | -set-names: list of names corresponding to the x-label of the plot.
• -top | -top-FE-results (optional - default=10): only plot the top n FE-change results.
• -fdr | -fdr-treshold (optional - default=0.01): sets the FDR treshold of the GO groups.

Example

Files used in this example are saved in the demo folder of this repository

Go to PantherDB-GO for plants (https://www.arabidopsis.org/tools/go_term_enrichment.jsp), paste the demo_gene_list.txt, Choose Organism Arabidopsis thaliana and Choose desired GO Aspect.

Once the information is submitted, export the PantherDB data as Table:

The expected output running the following code

python3 GO_plot.py -i /home/[user]/.../panther_exported_table.txt -names cluster1 -o ./plot

should look like this(saved as a high dpi .pdf file):

AUTHOR/SUPPORT

Lucas Servi, [email protected]