study_pancreas_fat: Pancreas Fat Study Parameters

In icj/mecfun: MEC Microbiome Helpers

Description

Set global variables for the MEC Pancreas Fat paper

Usage

study_pancreas_fat(main_var = "OMRI_NAFPD_55",
  main_var_cols = c("dodgerblue", "red"),
  main_cont = "OMRI_pct_panc_fat_corr",
  dir_out = "Output/Pancreas-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 = "PF", study_title = "Pancreas Fat",
  study_sent = "Pancreas fat", sg = "pancreas fat", q_cut = c(phylum
  = 0.2, genera = 0.05), cf = "_bookdown-pancreas-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.