Visualization of eggnog outputs?

eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

http://eggnog-mapper.embl.de

GNU Affero General Public License v3.0

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Visualization of eggnog outputs? #337

Closed JSSaini closed 2 years ago

JSSaini commented 3 years ago

Thank you for the tool. Is there a simple way to visualize eggnog outputs? Any already prepared script? Thanks.

Cantalapiedra commented 3 years ago

Hi @JSSaini ,

thank you for your kind words.

We really want to include some visualization options in future versions of eggnog-mapper (standalone and web). Unfortunately, we don't have any prepared script for this yet. Depending on which annotation (KEGG, GO, PFAM) or type of experiment (one sample, several samples, genome, metagenome) you may wish to rely on different tools for this purpose (KEGG mapper for instance).

I hope this makes sense and sorry for the inconveniences.

Best, Carlos

AnaMariaCabello commented 2 years ago

Hi, I'm using the last version of eggnog-mapper. It's a very nice tool! I'm trying to load into R the annotation table that I got as output, but It cannot be read properly as columns are separated by several and not fixed number of spaces. For instance 1 get one row with 23 columns and a different one with 26 (see the attached screenshot as example of the warning message). Is there a way in the eggnog-mapper command line to specify the format of the output as .csv, .txt or similar? The annotation file is very large (1G) so I cannot easily open it on my laptop to manipulate it.

I'm using eggnog to annotate ORFs from metagenomic samples that i previously predicted with PRODIGAL. This is my command line: emapper.py --cpu 32 -i ORF_prodigal.fasta --itype CDS --translate --output genecatalog --output_dir temp_data

Cantalapiedra commented 2 years ago

Hi @AnaMariaCabello ,

Thank you for your kind words.

If I am not mistaken, the ".emapper.annotations" file from emapper.py should have columns separated strictly by TAB, no by single whitespaces. What code are you using to load the table into R?

Best, Carlos

AnaMariaCabello commented 2 years ago

Hi Carlos,

You are right, the files are TAB separated and I was using the wrong function to load the table in R. Thanks a lot for your quick reply!

Ana

On Oct 17, 2022, at 3:42 PM, Carlos P Cantalapiedra @.***> wrote:

Hi @AnaMariaCabello https://github.com/AnaMariaCabello ,

Thank you for your kind words.

If I am not mistaken, the ".emapper.annotations" file from emapper.py should have columns separated strictly by TAB, no by single whitespaces. What code are you using to load the table into R?

Best, Carlos

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Cantalapiedra commented 2 years ago

Glad to be of help!

JSSaini commented 1 year ago

Hi, did any of you manged to visualize eggNOGG results including in R?

JSSaini commented 1 year ago

Hi, did any of you manged to visualize eggNOGG results including in R?

iliapopov17 commented 2 weeks ago

Hi, did any of you manged to visualize eggNOGG results including in R?

Recently I also wondered how to better visualize eggNOG-maperr's results. I found no better option than to write my own script. KEGGaNOG connects eggNOG-mapper and KEGG-Decoder and visualizes KEGG Pathways in heatmap format Available at this link: https://github.com/iliapopov17/KEGGaNOG Can be installed via pip Still working on the README