Usually I just try to work in R and Python. But sometimes, especially with Panel Figures cowplot isn't enough. So Illustrator and PowerPoint will get used from time to time :)
Thank you very much again for all the very informative videos. I was wondering if also order by Phylum and provide a colour bar on the left to indicate Phylum that the OUT is associated with.
Hi Pat, thanks for the great videos. I see in this video (and the few previous videos) that you plot OTUs/species. Do you know a set of commands that will collate E.g. all Lactobacillus OTUs and then plot those as one, and then the same for all Genus? I’ve spent a couple of days trying (coding newbie) but to no prevail. I have resorted to manually editing my input files (.subsample & .taxonomy) to collate the OTUs. I’m sure there is a quicker way to do this!! Thanks in advance for any help :)
Hey James - thanks for watching! You'll want to do a group_by and summarize to aggregate the counts together. I show how to do this in the minimalR materials. The relevant stuff is here... riffomonas.org/minimalR/09_taxonomic_data.html
Hmmm. Not sure what happened to the other comments. I’m aware of it but ... my general feeling about packages is that I’d rather learn a few that I use a lot really well than a bunch that I use rarely. I can’t keep all the syntax straight in my head. So I’m not super motivated to learn a niche package to do something we can do with existing tools. It’s a trade off!
How much processing of figures do you do outside of the software you use to generate the the figure?
Usually I just try to work in R and Python.
But sometimes, especially with Panel Figures cowplot isn't enough.
So Illustrator and PowerPoint will get used from time to time :)
Be sure to check out patchwork. I did a video on it a few weeks ago and compared it to cowplot. I think it’s a bit more powerful and easy to use
These videos, especially this one, has been super-helpful. Thanks!
My pleasure!
Thank you very much again for all the very informative videos. I was wondering if also order by Phylum and provide a colour bar on the left to indicate Phylum that the OUT is associated with.
You could order them by phylum by using the factor function and probably add the bars with geom_segment with clip=“off” in coord_cartesian
@@RiffomonasThank you so much, Pat. I appreciate your help.
Hi Pat, thanks for the great videos. I see in this video (and the few previous videos) that you plot OTUs/species. Do you know a set of commands that will collate E.g. all Lactobacillus OTUs and then plot those as one, and then the same for all Genus? I’ve spent a couple of days trying (coding newbie) but to no prevail. I have resorted to manually editing my input files (.subsample & .taxonomy) to collate the OTUs. I’m sure there is a quicker way to do this!! Thanks in advance for any help :)
Hey James - thanks for watching! You'll want to do a group_by and summarize to aggregate the counts together. I show how to do this in the minimalR materials. The relevant stuff is here... riffomonas.org/minimalR/09_taxonomic_data.html
Seems my other comment was removed twice...
Did you check out the package "ggsignif" ?
Hmmm. Not sure what happened to the other comments. I’m aware of it but ... my general feeling about packages is that I’d rather learn a few that I use a lot really well than a bunch that I use rarely. I can’t keep all the syntax straight in my head. So I’m not super motivated to learn a niche package to do something we can do with existing tools. It’s a trade off!