In today’s episode of Code Club, Pat Schloss demonstrates how you can create publication quality figures in R using ggplot2 and the rest of the tidyverse. We’ll then see how to insert that figure into an R markdown document that we will eventually submit to a journal for publication.
This episode is part of a larger arc of episodes investigating the sensitivity and specificity of amplicon sequence variants (ASVs), also known as exact sequence variants (ESVs) and operational taxonomic units (OTUs). ASVs are growing in popularity for analyzing microbial communities using 16S rRNA gene sequences. Proponents think that they should supplant operational taxonomic units (OTUs). What do you think? Pat demonstrates these concepts by live coding at the command line interface using GitHub Flow, Make, and RStudio.
The accompanying blog post can be found at http://www.riffomonas.org/code_club/2021-01-25-publication-quality-figures
4:44 Critiquing ESV(ASV) rate figure
8:39 Creating script to build figure
11:16 Setting format and size
15:52 ASV rate calculation
17:57 Figure labels and axes
19:57 Relabelling each facet
28:08 Outputting figure
29:52 Making script executable
32:15 Embedding into manuscript