how to make proportion plots with the latest QIIME2 version

Can you point to me where are the scripts to make a proportional plot using QIIME 2 202.2? I can find the scripts to make a heatmap but not the proportional plot.

Thank you!
Francesca

Hi @ranocchia,

could you clarify with an example what type of plot do you refer with proportional, please? I am not sure I am following you.

Still … to give you my best guess, the ‘taxa barplot’ plug in (https://docs.qiime2.org/2020.2/plugins/available/taxa/barplot/) visualises the taxonomy abundances as proportion of the total abundance for that sample into a bar-chart. Please note that the data are ‘relative’ cunts only on the plot, if you download the table form there you will have absolute count.

A different option could be to convert the absolute count in the feature artefact into relative counts using the ‘feature-table relative-frequency’ plug in (https://docs.qiime2.org/2020.2/plugins/available/feature-table/relative-frequency/). If you then export the data from there with the ‘tools export’ plug in you should obtain the same data in biom format. Finally, you can convert the biom table into a tab-delimited file by using the ‘biom convert’ command (if you using qiime2 conda environment is already installed, https://biom-format.org/documentation/biom_conversion.html). At this point you can load the table into your preferred plotting tool.

Hope this make sense.
Cheers

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