From 191d1f9ce44eb4d9f5ebfc9d3110a37798e1424a Mon Sep 17 00:00:00 2001 From: "Jacob T. Nearing" Date: Thu, 21 Nov 2024 15:07:27 -0500 Subject: [PATCH] Fixed logging file for new balanced parameter --- man/maaslin_log_arguments.Rd | 8 +++++++- tests/testthat/test_maaslin_log_arguments.R | 3 ++- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/man/maaslin_log_arguments.Rd b/man/maaslin_log_arguments.Rd index 94b69e3..4af9293 100644 --- 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 index db53dc7..925d7d6 100644 --- 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)