In this episode of Code Club, we'll show how you can call another program from within R using the system function. We'll call the lefse function from the mothur software package. Pat will then create an LDA score plot with ggplot2 and discuss the strengths and weaknesses of this popular data visualizaton technique.
Pat will use RStudio, the #system function and the #geom_col function from the #ggplot2 package to create the LDA score plots. The accompanying blog post can be found at https://www.riffomonas.org/code_club/2021-06-10-lefse.
The paper describing lefe can be found here: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-6-r60
Do you have a figure that you would like to receive a critique or help improving? Let me know and I'd be happy to arrange a guest appearance!
If you're interested in taking an upcoming 3 day R workshop, email me at [email protected]!
R: https://r-project.org
RStudio: https://rstudio.com
Raw data: https://github.com/riffomonas/raw_data/releases/latest
Workshops: https://www.mothur.org/wiki/workshops
You can also find complete tutorials for learning R with the tidyverse using...
Microbial ecology data: https://www.riffomonas.org/minimalR/
General data: https://www.riffomonas.org/generalR/
0:00 Introduction
5:34 Creating files to run lefse
10:03 Installing mothur and running in R/Rstudio
13:53 Creating function to setup files and run lefse
16:53 Creating lefse LDA plot
19:32 Improving appearace of LDA plot
24:34 Critique of LDA plots