Hi, can someone suggest a method for visualizing ANCOM-BC results? Specifically, am interested in plotting bar plots to show taxa found to be differentially abundant (based on q values). The current ANCOM-BC barplots plugin plots those considered significant based on p values, but need to plot corrected p values (q values). Thanks so much for your help!
Great question! We don't currently have any visualizers in our core distribution for barplots based on q-values. Maybe one of our forum @moderators have suggestions for third party tools that could be used for this?
Yes, a suggestion for third party tool would be much appreciated!
My apologies as I overlooked this in
da-barplot within q2-composition - the default is to plot q-values (not p-values). So this should be exactly what you need
Thanks! Strangely, when I hover over many of the bars that are plotted on the da-barplot output, ASV's with q>0.05 have been plotted... Related question, in the tabulate file, the q value is in the second column on that page (ie, not the value under the intercept column, correct)? Thanks again!
The default is that all features are plotted (both significant and insignificant). You can provide a threshold by passing
--p-significance-threshold. For example, if you provide
--p-significance-threshold 0.01, it will only plot features that achieved a q-value less than or equal to 0.01.
(Note, just to avoid possible confusion: the
--p-significance-threshold, indicates that this is a parameter to this visualizer, it's not indicating that this is a p-value significance threshold.)
That worked. Thank you everyone for your assistance. Really appreciated.