how to visualise log-ratios of features with Qurro

Hi all,
this might be an easy question for you, but I am completely lost.
I got some nice results: [Pseudo Q-squared: 0.417849 with Songbird BUT I do not know how to access Qurro and place the settings.
There is no plugin for Qurro in Qiime2-2020.2. Could somebody be so kind and give a step-by-step explanation how to proceed.
many thanks in advance for your kind help

Hi @rotifer,

Qurro isn’t a “core” QIIME 2 plugin, so you will need to install it independently. You can do this by (within your QIIME 2 environment) running the following commands:

pip install qurro
qiime dev refresh-cache

Once these are done, you should be able to use Qurro through QIIME 2! (I think you’ll want to use the command qiime qurro differential-plot, in particular; see here for some Qurro tutorials that may be helpful.)

Let us know if this works for you! :qiime2:

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Hi Fedarko,
I have 2 interesting error messages for you
I did as you recommended but numpy and cython were missing whose I installed with pip install but then this:
ERROR: scikit-bio 0.5.6 has requirement pandas>=1.0.0, but you’ll have pandas 0.25.3 which is incompatible.
ok, no problem: pip install pandas==1.0.3
but then
ERROR: qurro 0.6.0 has requirement pandas<1,>=0.24.0, but you’ll have pandas 1.0.3 which is incompatible.

how to solve this?

Hi @rotifer,

Those errors seem strange to me, since numpy, cython, and pandas should already be installed in QIIME 2 2020.2. I’m guessing you need to activate your QIIME 2 conda environment before running these commands; could you try that and let us know how that goes?

For reference, the second error is happening because Qurro doesn’t support pandas version 1 yet. If you’re using a QIIME 2 2020.2 environment then this probably shouldn’t be a problem, because the default pandas version in this version of QIIME 2 is 0.25.3.

Thanks!

Hi Fedarko,
many thanks for your fast reply; everything went smoothly. Now comes the “hard” part, playing with Qurro.
many thanks again,
Ulrike

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