I am now applying ANCOM to find the distinct taxa between my samples. When I get the result, I am confusing about the detail of "clr" in the visualisation plot, like below:
I have search the forum and I guess the meaning of the x-axis is something like "fold change", to show how different of the taxa changed between groups. But I want to know how exactly to calculate the "clr".
More specifically, in the plot I shown, the red point has a W score of 20 and clr of 2.8. How does this "2.8" come from?
That's a great questions. As far as I can tell, the clr value shown here is the results of the centre log ratio transformation that's part of skbio.stats.composition.clr.
Of course, that doesn't answer the question, "Why would I want to know the center log ratio of this data".
Let's see if @mortonjt can offer some advice on making use of this CLR value.
Thanks for the reply. Actually I want to plot the graph by my own in R, but I found that I couldn't export the data from "Export as TSV". Anyway, thanks for your help and I can calculate by mu own, happy new year !!
Hi @Lennon_Lee, this is a known bug and should be fixed soon (possibly the next release of QIIME 2, occurring in January, but I don't want to make promises ).
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