ANCOM-BC da_barplot couldn't generate plot

[Alxdu (Alex)]

qiime version 2023.2

Hi qiime team. Thank you for making ancombc an official plugin.
I ran into an issue with the barplot visualization of differentials.

Used the composition ancombc and composition tabulate to generate differentials

However, the composition da_barplot fails to generate barplots in the qzv file

from qiime2.plugins.composition.visualizers import da_barplot
ancom_diff_abn_barplot = da_barplot(data=ancombc_differentials).visualization.save("ancombc_barplot.qzv")

[lizgehret]

Hi @Alxdu,

Thanks for reaching out! Happy to hear that you're using ANCOM-BC in q2-composition.

Could you share what operating system you're using, and how you have QIIME 2 installed? I'm wondering where this error is coming from in the R traceback:

System has not been booted with systemd as init system (PID 1).
Can't operate. Failed to connect to bus: Host is down

[Alxdu (Alex)]

Hi Liz. Thanks for the quick feedback.

I install qiime2 in Windows Subsystem for Linux running Ubuntu 22.04

On a broader comment about ancombc (as I have been using the un-official version from Morton in the past GitHub - mortonjt/q2-ancombc: qiime2 plugin for ANCOMBC), can I make a short feature request for the tabulate plugin. Can you please add the optional argument to sort and filter the table by lfc and/or q_val. Thank you very much.

I am also curious how the barplot is handled in this new ancom implementation. My own implementation of differential plotting with Morton's plugin was to place the lfc on the x-axis, the taxa on y-axis and the q_val on the secondary y-axis (sorted from 0 to 0.05), like this:

[lizgehret]

Hi @Alxdu,

Thanks for following up and providing those details!

@Alxdu

I install qiime2 in Windows Subsystem for Linux running Ubuntu 22.04

I found what seems to be a pretty helpful thread on AskUbuntu that discusses the error message you're receiving in detail and a few ways to solve it or move forward. Check it out and see if this helps!

System has not been booted with systemd as init system (PID 1). Can't operate

@Alxdu

can I make a short feature request for the tabulate plugin. Can you please add the optional argument to sort and filter the table by lfc and/or q_val. Thank you very much.

This is a great suggestion, and is definitely on our radar! The current version of tabulate is our first iteration, and I would definitely like to add filtering and sorting capabilities to it as well. We have a lot on our plates for the 2023.5 release, but hopefully this is something we can address over the summer!

@Alxdu

I am also curious how the barplot is handled in this new ancom implementation.

This implementation uses the log-fold change on the x-axis, and the feature-id's on the y-axis. You can view an example visualization here for reference:
https://view.qiime2.org/visualization/?type=html&src=https%3A%2F%2Fdl.dropbox.com%2Fs%2Fr7j8pvyv604ynrz%2Fq2comp-104-example-output.qzv%3Fdl%3D1

Cheers

[Alxdu (Alex)]

Thanks Liz. I'll give this a try and provide feedback here. Looking forward to where you take this plugin. It's already great. Thank you for the work you do for the community.