Xenome: show percentages by default, add table and sections

[vladsavelyev]

Few adjustments to the Xenome module based on the feedback from @tamuanand (including #1860 (comment))

1. In the table columns and plots, showing the percentages by default:

2. Added a summary table in addition to the general stats columns. Added there hidden columns for read counts.

3. Properly added section wrappers to the plots to make sure they appear in the contents panel.

4. Additionally, making sure that the color scales for species in the table match the colors in the bar plot.

[github-actions]

🚀 Deployed on https://mqc-pr-2164--multiqc.netlify.app

[tamuanand]

Thanks a ton @vladsavelyev for working on this.

[tamuanand]

@vladsavelyev One suggestion - to add to the multiqc docs for xenome

xenome classify outputs useful stats to stderr/stdout

• hence once has to redirect command line output to a sample_name.xenome_stats.txt file for MultiQC to parse this useful info (very much like how it is done for kallisto - https://mqc-pr-2164--multiqc.netlify.app/modules/kallisto/)
• also the tool does not register any sample name info in this stderr/stdout - hence it is very important to correctly name the stdout/stderr file
• do not do this - naming the stdout/stderr file as xenome_stats.txt without any sample name prefix would lead to input file collision when one is bringing together files from xenome runs on multiple samples and then running multiqc on it

[ewels]

LGTM to merge after the suggested docs additions are made 👍🏻

[tamuanand]

@vladsavelyev is this available in a dev version that I can try out after installing with pip like this?

pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git

[vladsavelyev]

@tamuanand, after the PR is merged - yes. Before that, you would need to specify the branch name as well:

pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git@xenome

If you do it often though, it's convenient to keep a clone of the repo locally:

git clone https://github.com/ewels/MultiQC.git

And run pip install -e MultiQC, so the multiqc installation uses the exact locally cloned code base in the MultiQC folder.

You can optionally check out a specific branch:

cd MultiQC
git checkout xenome

And you installation will switch into it automatically without need to do pip install again.