Merge pull request #1 from biobakery/maaslin3_code_cleanup

Maaslin3 code cleanup
biobakery · Aug 3, 2024 · 7764a34 · 7764a34
2 parents 3d05ca7 + de2df45
commit 7764a34
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Showing 3 changed files with 6 additions and 24 deletions.
diff --git a/R/fit.R b/R/fit.R
@@ -1,15 +1,4 @@
 #!/usr/bin/env Rscript
-# Load Required Packages
-for (lib in c(
-  'dplyr',
-  'pbapply',
-  'lmerTest',
-  'parallel',
-  'lme4',
-  'multcomp'
-)) {
-  suppressPackageStartupMessages(require(lib, character.only = TRUE))
-}
 
 # Function to augment data for logistic fitting
 augment_data <- function(formula, random_effects_formula, dat_sub){

diff --git a/R/maaslin3.R b/R/maaslin3.R
@@ -24,12 +24,6 @@
 # THE SOFTWARE.
 ###############################################################################
 
-# load in the required libraries, report an error if they are not installed
-
-for (lib in c('optparse', 'logging', 'data.table', 'dplyr')) {
-    suppressPackageStartupMessages(require(lib, character.only = TRUE))
-}
-
 ###############################################################
 # If running on the command line, load other Maaslin3 modules #
 ###############################################################
@@ -44,8 +38,12 @@ if (identical(environment(), globalenv()) &&
         sub("--file=", "", script_options[grep("--file=", script_options)])
     script_dir <- dirname(script_path)
     script_name <- basename(script_path)
-
-    for (R_file in dir(script_dir, pattern = "*.R$"))
+    R_files <- c("fit.R", "utility_scripts.R", "vis.R")
+    # load in the required libraries, report an error if they are not installed
+    for (lib in c('optparse', 'logging', 'data.table', 'dplyr', 'pbapply','lmerTest','parallel','lme4','multcomp','ggplot2','viridis',"grid",'RColorBrewer','patchwork','scales')) {
+        suppressPackageStartupMessages(require(lib, character.only = TRUE))
+    }
+    for (R_file in R_files) 
     {
         if (!(R_file == script_name))
             source(file.path(script_dir, R_file))

diff --git a/R/viz.R b/R/viz.R
@@ -23,11 +23,6 @@
 # THE SOFTWARE.
 ###############################################################################
 
-# Load libararies
-for (lib in c('dplyr', 'ggplot2', 'viridis', "grid", 'RColorBrewer', 'patchwork', 'scales')) {
-    suppressPackageStartupMessages(require(lib, character.only = TRUE))
-}
-
 # MaAsLin3 theme based on Nature journal requirements
 nature_theme <- function(x_axis_labels, y_label) {
     # set default text format based on categorical and length