LeyLab R misc

Misc R functions, rmarkdown templates, etc. for making life a bit easier in the Ley Lab

Feel free to contribute! Just clone the repo, make some changes, commit, and create a pull request.

Contributors

• Nick Youngblut [email protected]
• Jacobo de la Cuesta [email protected]
• Albane Ruaud [email protected]

Install

renv R package

renv::install("leylabmpi/LeyLabRMisc")

devtools R package

devtools::install_github("leylabmpi/LeyLabRMisc")

source() function

• Clone the repo: git clone [email protected]:leylabmpi/LeyLabRMisc.git
• In your R session, use source("path/to/repo/init.R")
  • Note: you will need to source each *.R file individually

Submodules

• If this repo will be inside another git repo, then use git submodule
  • See this stack overflow post

Function overview

• General functions for table + plot formatting
• Functions for reading/writing files
• Functions for running bash commands (with conda)
• Functions to help with cluster job submission
• Functions for creating iTOL input
• Functions for machine learning
• Functions for multivariate data analysis
• Functions to help with using the phyloseq R package
• Functions to help process metagenome profiling data
• Functions to interface with the MGnify and ENA APIs

Manual & Tutorials

• Manual pdf
• Jupyter notebooks
  • general commands

Templates

Rmarkdown templates are in inst/rmarkdown/templates/

To use a template:

• Install this package
• Restart R
• Go to File => New File => R Markdow ... => From Template

Examples

Metagenomes

Reading in bracken tables

library(dplyr)
library(ggplot2)
library(data.table)
library(tidytable)
library(LeyLabRMisc)

# listing files
brk_cls_files = list_files(profile_dir, 'all-combined-bracken.tsv') 
brk_cls_files %>% length
# reading tables
brk_cls = brk_cls_files %>% file_list(-2) %>%
    plyr::llply(read_bracken) %>%
    data.table::rbindlist(use.names=TRUE, idcol='dataset')
brk_cls

TODO