study_ancestry: Genetic Ancestry Study Parameters

In icj/mecfun: MEC Microbiome Helpers

Description

Set global variables for the MEC Characterization paper

Usage

study_ancestry(main_var = "anc_max", main_var_cols = c("#A6CEE3",
  "#1F78B4", "#B2DF8A", "#33A02C", "#FB9A99", "#E31A1C", "#FF7F00",
  "#6A3D9A"), main_cont = "", dir_out = "Output/Ancestry",
  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 = "mGWAS",
  study_title = "Ancestry", sg = "ancestry", q_cut = c(phylum = 0.05,
  genera = 0.05), zhern_cols = viridis::viridis(10),
  zhern_names = c("Demographics", "Alcohol", "Anthropometric measures",
  "Special diet", "Cultural foods & dietary components",
  "Dietary quality index", "Medical conditions", "Medications",
  "Physical activity", "Smoking"), 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
sg	Lowercase study group name
q_cut	FDR cutoffs for phylum and genera
zhern_cols	Colors for Zhernakova categories
zhern_names	Names of Zhernakova categories
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.