study_liver_fat: Liver Fat Study Parameters

In icj/mecfun: MEC Microbiome Helpers

Description

Set global variables for the MEC Liver Fat paper

Usage

study_liver_fat(main_var = "OMRI_NAFLD_55",
  main_var_cols = c("dodgerblue", "red"),
  main_cont = "OMRI_pct_liver_fat_corr", dir_out = "Output/Liver-Fat",
  dir_dta = file.path(dir_out, "Data"), dir_dwn = file.path(dir_out,
  "Downloads"), dir_fig = file.path(dir_out, "Figures"),
  dir_tab = file.path(dir_out, "Tables"), study_filter = "LF",
  study_title = "Liver Fat", study_sent = "Liver fat",
  sg = "liver fat", q_cut = c(phylum = 0.05, genera = 0.05),
  cf = "_bookdown-liver-fat.yml", run_code = FALSE,
  download_files = TRUE)

Arguments

main_var	Main study categorical variable
main_var_cols	Colors for main study varible
main_cont	Main study continuous variable
dir_out	Output directory
dir_dta	Output directory for data objects
dir_dwn	Output directory for downloadable files
dir_fig	Output directory for figures
dir_tab	Output directory for tables
study_filter	Study indicator for filtering to appropriate samples
study_title	Formal study title
study_sent	Study title for sentence
sg	Lowercase study group name
q_cut	FDR cutoffs for phylum and genera
cf	bookdown config file
run_code	Run scripts during book build
download_files	Create downloadable file links

Value

Variables are saved to the global environment.

icj/mecfun documentation built on Nov. 4, 2019, 1:54 p.m.