This repository contains the materials and code required to create a relative abundance barplot as described in this video.
The data plotted corresponds to bacterial abundance that live in the soil, rhizospher (R) and endophytic compartment (E) of Arabidopsis thaliana plants. The data is a small subset of the dataset that was published here.
These materials were created for the 2022 SFSU Science Coding Immersion Program (SCIP) & Promoting Inclusivity in Computing (PINC) summer pograms.
In order to follow this tutorial you just need R with the tidyverse package installed. If you haven't installed the tidyverse yet, simply open an R session and type:
install.packages("tidyverse")It is also recommended to have RStudio installed although you can use any platfform that allows you to run R code.
The code in the video and the extended example requires the three files in the subdirectory data/rhizo. Those files correspond to the OTU table, the OTU taxonomy, and the sample metadata and they must be in the machine where you are running the R code.
There is additional files in the data/hmp_v13 subdirectory. The files there have the same names as the files in data/rhizo, but correspond instead to a subset of the data from the Human Microbiome Project. The data in these files was downloaded from this repository and the files are formatted so that they will match the format of the rhizospher dataset. Thus, these files can be analyzed with the same code in order to explore a different host-microbe system.
The extended example provides additional details about the code and data used in the workshop. The extended example is in the file extended_example.md. The RMarkdown code that generated that filee is at extended_example.Rmd
Hera are some additional excerscises that you can do to practive what you learned in this workshop:
-
You learned how to sort the taxonomic groups in the barplot, can you sort the samples by relative Proteobacteria abundance? can you reverse the order of the facets?
-
Look a the extra files at data/hmp_v13. Can you make a plot showing the bacterial taxonomic distributions in human stool and Saliva, are there any differences by sex?
-
For any questions just raise an issue in this repository
-
Slides from the workshop video.
-
Video of the workshop.
-
Code typed during the video.
(C) Copyright 2022 Sur Herrera Paredes
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.