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

30 views
Skip to first unread message

jiakang yin

unread,
Nov 13, 2019, 3:55:37 AM11/13/19
to HUMAnN Users
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

unread,
Nov 18, 2019, 3:46:49 PM11/18/19
to humann...@googlegroups.com
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:


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.

--
You received this message because you are subscribed to the Google Groups "HUMAnN Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to humann-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/humann-users/909a4149-e286-4637-8ed9-83f542e145e1%40googlegroups.com.
Reply all
Reply to author
Forward
0 new messages