adjusted analysis ancom

[kimshinseung (ss)]

Hi I did an analysis in R for ancom adjusted analysis.
By the way, I don't know how to get the result of PLOT provided by QIIME2. I would appreciate it if you could tell me how to get VOLCANO PLOT.

[Mehrbod_Estaki]

Hi @kimshinseung,
Sorry but it's not very clear what are you asking for. Could you please clarify with a bit more detail please?
You used ANCOM or ANCOM2 in R? What do you mean by 'adjusted analysis'?
Which PLOT are you referring to in Qiime2? Which Qiime2 version? What command did you run exactly to create your plot?
The qiime2 ancom plugin provides you with a visualizer that has the volcano plots. Follow this example from the Moving Pictures tutorial for instance. You can download the plot itself in SVG or PNG format by clicking the buttons on the top of the visualizer or download the raw data by clicking the TSV button there.

[kimshinseung (ss)]

Hello, I know that only ancom Standard analysis is possible in qiime2. (Adjusted analysis: I understand that the correlation analysis of the adjusted variables is not possible with qiime2 ancom.) So I want to know the command of volcano plots provided by qiime2 ancom. I want to use the volcano plots command of qiime2 in R.

[Mehrbod_Estaki]

Hi @kimshinseung,
Hmm, neither ANCOM (in q2) or ANCOM2 handle correlation analysis as far as I know. ANCOM2 can handle co-variables and longitudinal analysis, if that is what you are referring to. Though I'm not sure what the question of volcano plots code has to do with that...perhaps I'm not understanding what you're trying to do. But either way, to reproduce the volcano plots in R can be as easy or as complicated as you want it to be.
Once you download the raw TSV file from the q2-ancom visualizer, import it into R (here called data) and you can run something like this:
With base R:

plot(data[,2:3])

And you can add all the bells and whistles as you want.
Or if you're using ggplot, a very simple version could be:

sig.w<- data$W >50 #arbitrarily setting sig W value
data$sig.w <- sig.w
ggplot(data) +
        geom_point(aes(x=clr, y=W, colour=sig.w)) +
        ggtitle("Volcano Plot") +
        xlab("clr") + 
        ylab("W")

[shinseung]

Hi
I want to do the “co-variables” analysis you talked about.
Is it possible in qiime2?

[Mehrbod_Estaki]

Hi @shinseung,
As you mentioned earlier this type of analysis is not available in the qiime2 version of ANCOM but ANCOM2 in R can handle this, you can find more info on ANCOM2 on the author's personal page here.
In qiime2, another similar tool gneiss does allow covariables but works a bit differently than ancom. You can find a few tutorial for that here and here.