how to display all the KOs that were significant between control and treat

[jiakang yin]

after doing humann2_associate, we find many KOs are significantly enriched in the treat group. However, I have difficulty in the visualization of data. According to the manual, we can only choose one genefamily or pathway to get a barplot. Is there any way that is capable of showing all the PWY and their corresponding species that contribute to it. Like a circos? Thanks in advance.

[Eric Franzosa]

You could in principle write a loop at the command-line to do this. However, I would recommend using a more formal statistical analysis package rather than trying to do "fancy" things with the humann2_associate script (which is bundled largely for tutorial purposes). MaAsLin2 for example will produce books of figures based on analyses of HUMAnN2 tables with associated metadata:

https://huttenhower.sph.harvard.edu/maaslin2

Thanks,

Eric

On Wed, Nov 13, 2019 at 3:55 AM jiakang yin <yinjiak...@gmail.com> wrote:

after doing humann2_associate, we find many KOs are significantly enriched in the treat group. However, I have difficulty in the visualization of data. According to the manual, we can only choose one genefamily or pathway to get a barplot. Is there any way that is capable of showing all the PWY and their corresponding species that contribute to it. Like a circos? Thanks in advance.

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