From da354f768667ced53decdd4f82e794776970560c Mon Sep 17 00:00:00 2001
From: "Jacob T. Nearing" <nearing@broadinstitute.org>
Date: Wed, 20 Nov 2024 20:10:27 -0500
Subject: [PATCH] Updated man pages to include balanced parameter

---
 man/maaslin3.Rd                         | 8 +++++++-
 man/maaslin_plot_results.Rd             | 8 +++++++-
 man/maaslin_plot_results_from_output.Rd | 8 +++++++-
 3 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/man/maaslin3.Rd b/man/maaslin3.Rd
index 1f05bcd..d54e5df 100644
--- a/man/maaslin3.Rd
+++ b/man/maaslin3.Rd
@@ -57,7 +57,8 @@ maaslin3(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
@@ -210,6 +211,11 @@ maaslin3(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{
     A list containing the following items:
diff --git a/man/maaslin_plot_results.Rd b/man/maaslin_plot_results.Rd
index f3b7780..5e56902 100644
--- a/man/maaslin_plot_results.Rd
+++ b/man/maaslin_plot_results.Rd
@@ -32,7 +32,8 @@ maaslin_plot_results(output,
                     coef_plot_vars = NULL,
                     heatmap_vars = NULL,
                     plot_associations = TRUE,
-                    max_pngs = 30)
+                    max_pngs = 30,
+                    balanced=FALSE)
 }
 \arguments{
     \item{output}{The output folder to write results.}
@@ -95,6 +96,11 @@ maaslin_plot_results(output,
     associations.}
     \item{max_pngs}{The top \code{max_pngs} significant associations will be
     plotted.}
+    \item{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{
 Results will be written to the \code{figures} folder within the folder
diff --git a/man/maaslin_plot_results_from_output.Rd b/man/maaslin_plot_results_from_output.Rd
index 6eca110..9691402 100644
--- a/man/maaslin_plot_results_from_output.Rd
+++ b/man/maaslin_plot_results_from_output.Rd
@@ -32,7 +32,8 @@ maaslin_plot_results_from_output(output,
                                 coef_plot_vars = NULL,
                                 heatmap_vars = NULL,
                                 plot_associations = TRUE,
-                                max_pngs = 30)
+                                max_pngs = 30,
+                                balanced=FALSE)
 }
 \arguments{
     \item{output}{The output folder to write results.}
@@ -86,6 +87,11 @@ maaslin_plot_results_from_output(output,
     associations.}
     \item{max_pngs}{The top \code{max_pngs} significant associations will be
     plotted.}
+    \item{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{