figures - multispecies

[grace-ac]

Making some figures for the multi-species project.

There is no functional enrichment - I re-did it multiple times the past couple days to make sure I was getting the same result, and DAVID has consistently shown no enrichment.

So- making some figures to share with Drew.

First figure so far:

The shared GOslim terms across the three species, with counts of genes

[grace-ac]

This too:

Have to do some cleaning up in photoshop, but essentially showing the same thing as above plot, but in the circle form.

the three species are separated at the top half of circle
gene counts contributing to each of the GOslim terms from each species are the bands going down to the bottom half

the terms are listed on bottom - just need to be cleaned up in photoshop with the color label and GOID number for the terms to match the band color

[sr320]

You have a DEGs from three species.. For each species DEGs, make a pie chart with GO slim terms occurrence.

[sr320]

Essentially this https://github.com/RobertsLab/resources/issues/2369#issuecomment-3498337813

you have immune response on one species? and not other and this is not clear from figure above.

output @

https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/workflow-annotation/output/

Pycno

Derm

Pisa

[grace-ac]

Yep!

the top two figs i put are only showing what's shared.

per species, i'm trying out waffle plots --> learned in beautiful graphics in R that waffle plots or bar plots are more intuitive to compare categories than pie charts

here's a try at one for the GO categories with DEG counts for pycno, though i'm seeing that the terms are different from what your charts are, so i'm going to look into that now:

[sr320]

Please Please 🙏- humor me and make three pie charts with top go slim of DEGs…

On Fri, Nov 21, 2025 at 5:29 PM Grace Crandall @.***> wrote:

grace-ac left a comment (RobertsLab/resources#2379) https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2379*issuecomment-3565243028__;Iw!!K-Hz7m0Vt54!huw60_fb4EpjFDY-Fx8lLlm08vDo1wD1j3IZqsTs11XIbcP0CAMVoV89NW5f-z9pYNoDd2JEFpWqkTMAH7W81Jo$

Yep!

the top two figs i put are only showing what's shared.

per species, i'm trying out waffle plots --> learned in beautiful graphics in R that waffle plots or bar plots are more intuitive to compare categories than pie charts

here's a try at one for the GO categories with DEG counts for pycno, though i'm seeing that the terms are different from what your charts are, so i'm going to look into that now: image.png (view on web) https://urldefense.com/v3/__https://github.com/user-attachments/assets/d338c687-bdb8-45bc-828a-29aba6499cfe__;!!K-Hz7m0Vt54!huw60_fb4EpjFDY-Fx8lLlm08vDo1wD1j3IZqsTs11XIbcP0CAMVoV89NW5f-z9pYNoDd2JEFpWqkTMAvqmySd4$

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2379*issuecomment-3565243028__;Iw!!K-Hz7m0Vt54!huw60_fb4EpjFDY-Fx8lLlm08vDo1wD1j3IZqsTs11XIbcP0CAMVoV89NW5f-z9pYNoDd2JEFpWqkTMAH7W81Jo$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PN3BZ3U3LU6GBA2L7P33564ABAVCNFSM6AAAAACM3BWQZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKNRVGI2DGMBSHA__;!!K-Hz7m0Vt54!huw60_fb4EpjFDY-Fx8lLlm08vDo1wD1j3IZqsTs11XIbcP0CAMVoV89NW5f-z9pYNoDd2JEFpWqkTMAPgACvqc$ . You are receiving this because you commented.Message ID: @.***>

[grace-ac]

(working on getting this key smaller so the pie chart is larger):

[sr320]

Come on.... look at my bar charts. - "anatomical structure development" should be biggest proportion?... - and only plot top 13.

[sr320]

You can certainly make fancier - but this gets simple message across that some predominant processes in DEGs are common and some unique to one (bold) or two (underline).

[grace-ac]

[grace-ac]

[grace-ac]