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statdivlab / corncob

Count Regression for Correlated Observations with the Beta-binomial
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Visualizing corncob output #74

Closed kattihorng closed 4 years ago

kattihorng commented 4 years ago

Hi there! Our lab is really interested in using GraPhlAn to visualize differential abundances of our microbiome dataset. I'm having a hard time parsing the output from corncob into GraPhlAn. Would you be willing to include a function that parses the corncob output for GraPhlAn? I know this might be a lot to ask, but I think it would be a very useful pipeline for investigators doing microbiome research.

For example, Figure 1 of this paper is exactly what I'm hoping to visualize. Using a cladogram, the authors can compare increases and decreases in taxa (and different levels as well) from 2 experimental groups. They use LEfSe to create the input to GraPhIAn. I would really like to use the output from corncob, so your help is much much appreciated!

bryandmartin commented 4 years ago

Hi @kattihorng ,

I can potentially do this, but I would need more details about what sort of output you need, because I am not personally familiar with GraPhlAn's interface. Do you know the output that is required in order to use GraPhlAn?

Thanks for posting the issue! Bryan

taylorreiter commented 4 years ago

Hi @kattihorng and @bryandmartin! I was interested in this visualization as well, so I started looking into the GraPhIAn format. It's pretty...intense. So, I then began looking for an alternative. I have been able to produce a similar graphic using ggtree. I'm still doing some behind the scenes prep of my data to get it corncob compatible so I haven't tried it with the corncob output, but I think this might be a solution that is closer to out-of-the-box.

I'll check back in when I have a reprex, but the examples here could be a start: https://yulab-smu.github.io/treedata-book/chapter6.html#viewing-selected-clade

bryandmartin commented 4 years ago

Closing this due to inactivity. Thanks for the response @taylorreiter !

taylorreiter commented 2 years ago

Two years later and I finally implemented something similar to this request! It can be seen at the bottom of the post here: https://taylorreiter.github.io/2022-08-30-Visualizing-the-taxonomic-composition-of-metagenomes-using-sourmash-and-metacoder/