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KasperSkytte / ampvis2

Tools for visualising microbial community amplicon data
https://kasperskytte.github.io/ampvis2/
GNU General Public License v3.0
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amp_boxplots by OTUs? #99

Closed jarrodscott closed 3 years ago

jarrodscott commented 3 years ago

Hi there.

Is it possible to use amp_boxplots to display OTUs rather than aggregating by taxa? I have a low diversity data set with poor classification at lower ranks (i.e., Genus, species) so I would just like to display box plots for top OTUs. I have tried tweaking the various parameters but no matter what I do, I get back a plot with---for some reason---only really rare OTUs.

Maybe it doesn't make sense to display info in this way since we get similar outputs with amp_heatmap but I would like to compare the heatmap and boxplots. Thanks!

KasperSkytte commented 3 years ago

Hi

Have you set tax_aggregate = "OTU"? Keep in mind boxplots are sorted by median and heatmap by mean (though median probably makes more sense even for the heatmap, community data are rarely normally distributed)

jarrodscott commented 3 years ago

Hi @KasperSkytte

I did set tax_aggregate = "OTU" but the median v. mean was the issue. Thank you for clarifying. Problem solved.

KasperSkytte commented 3 years ago

Great!