Fixed logging file for new balanced parameter

biobakery · Nov 21, 2024 · 191d1f9 · 191d1f9
1 parent da354f7
commit 191d1f9
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git a/man/maaslin_log_arguments.Rd b/man/maaslin_log_arguments.Rd
@@ -47,7 +47,8 @@ maaslin_log_arguments(input_data,
                     max_pngs = 30,
                     cores = 1,
                     save_models = FALSE,
-                    verbosity = 'FINEST')
+                    verbosity = 'FINEST',
+                    summary_plot_balanced=FALSE)
 }
 \arguments{
     \item{input_data}{A data frame of feature abundances or read counts or a
@@ -185,6 +186,11 @@ maaslin_log_arguments(input_data,
     \item{save_models}{Whether to return the fit models and save them to an
     RData file.}
     \item{verbosity}{The level of verbosity for the \code{logging} package.}
+    \item{summary_plot_balanced}{If set to TRUE the summary plot will 
+    show the top N features of each variable included in 
+    \code{coef_plot_vars} where N is equal to: 
+    \code{ceiling(summary_plot_first_n/length(coef_plot_vars))}. Will error
+    if \code{coef_plot_vars} = \code{NULL}}
 }
 \value{
     No value is returned, but a logger is opened with the parameters logged.

diff --git a/tests/testthat/test_maaslin_log_arguments.R b/tests/testthat/test_maaslin_log_arguments.R
@@ -41,7 +41,8 @@ maaslin_log_arguments(input_data = 'something1',
                       max_pngs = 8,
                       cores = 9,
                       save_models = FALSE,
-                      verbosity = 'FINEST')
+                      verbosity = 'FINEST',
+                      summary_plot_balanced=FALSE)
 
 lines_in <- readLines(file.path(output_tmp, 'maaslin3.log'))
 lines_in <- sub('.*::', '', lines_in)