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DessimozLab / OMArk

GNU Lesser General Public License v3.0
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Companion script for combined plot? #9

Closed dirkjanvw closed 1 year ago

dirkjanvw commented 1 year ago

Hi, thanks for making this great tool available! I was wondering whether it would be possible to include a companion script to produce a combined plot for a couple runs. In your preprint, Figure 4, 5A and 5B have such a plot but I cannot discover a script to produce it on your GitHub. I was hoping to find something like the generate_plot.py script that BUSCO has. Would it be possible to include such a script here?

YanNevers commented 1 year ago

Thank for your nice comment and your interest!

I agree this is an important feature to visualize the data of multiple species. I only need to do a slight reworking of the code I used on the manuscript for the Figure you mentioned. Once it is done, I will upload it (in a few days at most) here, likely as a companion script and as an interactive Jupyter Notebook. I'll let you know when it is done.

YanNevers commented 1 year ago

Hi @dirkjanvw

A companion script is now available on the utils folder of this repo (plot_all_results.py). It will generate plots similar to the one we present in the manuscript from a folder containing several OMArk output folders. It is also possible to interface with the data interactively using the associated Jupyter Notebook.

I plan to add more feature with time but I hope this version will be functional enough already. Let me know if you have any issue with it.

dirkjanvw commented 1 year ago

Hi @YanNevers

Thanks a lot for providing this script! I really appreciate the effort :)

I have only found one small bug in it: I named my OMArk output folders after species names and I found out that sometimes this caused a mismatch between the first column of the mapping file and the actual name (e.g. helianthus_annuus became helianthus_ann). I fixed it in a fork I just created (as well as some small typos I discovered since I made the fork anyways). I will make a pull request in a couple minutes after commenting this, so you can see what I think would be the best fix.

YanNevers commented 1 year ago

Hi @dirkjanvw

Thank you for reporting the bug, suggesting changes and even fixing typos! This is much appreciated! I agree your solution is a good fix so I just merged your fork into the main branch.

I am now closing the issue but feel free to reach out again if have other features requests.