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biocore / mmvec

Neural networks for microbe-metabolite interaction analysis
BSD 3-Clause "New" or "Revised" License
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heatmap change "--p-x-labels " size #156

Closed iratxezarra closed 3 years ago

iratxezarra commented 3 years ago

Hello developpers!

I am able to successfully create several heatmaps, but i am working with aprox. 80-90 metabolites and I can't find a way of displaying all the their names in the x axis. Is there a way of decreasing the size of the labels?

Also, I was not able to find additional information regarding which is the difference between conditional.qza and ranks.qza, ( if there is any).

Thanks so much for the help and for developing such a nice tool!

mortonjt commented 3 years ago

Hi @iratxezarra thank you for your interest.

The plotting abilities for mmvec are a bit limited, since its not a plotting library. But you can always export your data to be read in Python / R; you can convert your conditional.qza / ranks.qza to a text file as follows

qiime tools export --input-path ranks.qza --output-path ranks-text

P.S. conditional.qza and ranks.qza are likely the same type; you can check with qiime tools peek

iratxezarra commented 3 years ago

Thanks for answering! i will try to create the heatmaps in R then! conditional.qza and rank.qza are same type, yes, but is it the same information but sorted, or what is the difference between the numbers that appear in both documents?

Iratxe Zarraonaindia Martinez Maria Goyri, Lab. 1.08. (Applied genomics and Bioinformatics) University of the Basque Country (UPV/EHU) Bº Sarriena s/n 48940, Leioa; Bilbao; Spain Tfno: +34-946015510 E-mail: @., @. http://www.genomic-resources.eu/

El mié, 7 abr 2021 a las 17:09, Jamie Morton @.***>) escribió:

Hi @iratxezarra https://github.com/iratxezarra thank you for your interest.

The plotting abilities for mmvec are a bit limited, since its not a plotting library. But you can always export your data to be read in Python / R; you can convert your conditional.qza / ranks.qza to a text file as follows

qiime tools export --input-path ranks.qza --output-path ranks-text

P.S. conditional.qza and ranks.qza are likely the same type; you can check with qiime tools peek

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mortonjt commented 3 years ago

I'm not exactly which files you are referring to, since the filenames are specified by you. They should both output mean-centered log conditional probabilities. If you want raw conditional probabilities, see https://github.com/biocore/mmvec/issues/93