Clarification on RELAX Analysis Output Visualization

[aaannaw]

I am currently conducting a RELAX analysis on 13,057 orthologous genes and have encountered some questions regarding the interpretation of the output, particularly when using the HyPhy Vision tool (https://veg.github.io/hyphy-vision/relax/#). I would greatly appreciate your assistance with the following points:
(1) Error while Uploading JSON File: I attempted to upload one of my JSON files to the website, but I encountered the error message.

(2) Meaning of the Arrows in the Example Plot: In the example plot provided on the website, there are arrows present. Could you kindly explain what these arrows represent?

(3) Plotting for All Genes vs. Individual Genes: I would like to confirm whether it is possible to generate a plot that summarizes the results for all genes, or if the visualization is restricted to individual plots per gene. I have seen in several publications, such as Correlated Evolution of Social Organization and Lifespan in Mammals (2023), that plots for all genes in the test and reference branches are displayed. Is this possible using the HyPhy Vision tool?

I look forward to your response and any guidance you can provide. Thank you for your time and assistance.

Best regards,
Na Wan

[spond]

Dear @aaannaw,

1. Unfortunately, the vision page is a bit obsolete. Could you possibly share the JSON file that triggered the error message? I may have a solution.
2. The arrows are simply there as a visual cue (springs); they connect corresponding ω values in test and reference distributions.
3. This seems to be a plot developed by the paper authors (and it's for individual genes). It's not too different from what's in HyPhy vision.

Best,
Sergei

[aaannaw]

Dear author,
Thanks for your response.
The JSON file is attached:
evm.model.ptg000001l.10.fa.RELAX.json
I believe the useful information in the RELAX output JSON file includes the K value, P value, and the three omega values for both the test and reference branches in the RELAX alternative model. To analyze this, I wrote a Perl script to extract these parameters from the JSON file for each gene and then calculate the median value for each parameter across all genes.
The resulting plot is shown below:

Unfortunately, I was unable to modify the code to make the x-axis ticks display at equal intervals, similar to the format seen on the website. Could you please help with this issue?

Best regards,
Na Wan