From df1e66e918f898b2d70a74c8127da2e5196d6a7a Mon Sep 17 00:00:00 2001
From: stnava <stnava@gmail.com>
Date: Mon, 12 Aug 2024 09:25:59 -0400
Subject: [PATCH] COMP: plot_features example

---
 R/multiscaleSVDxpts.R   | 4 ++++
 man/plot_features.Rd    | 2 ++
 man/simlr.parameters.Rd | 4 ++++
 3 files changed, 10 insertions(+)

diff --git a/R/multiscaleSVDxpts.R b/R/multiscaleSVDxpts.R
index 323a2d58..1d5ee178 100644
--- a/R/multiscaleSVDxpts.R
+++ b/R/multiscaleSVDxpts.R
@@ -4374,6 +4374,8 @@ vector_to_df <- function(vector, column_name) {
 #' @param positivities_options A list of options for the `pizzer` parameter.
 #' @param optimus_options A list of options for the `optimus` parameter.
 #' @param constraint_options A list of options for the `constraint` parameter, default is `list("none")`.
+#' @param num_samples if not full, then the size of the subset space
+#' @param search_type string vector either full random or deterministic
 #' 
 #' @return A list containing all (or a subset of) combinations of the provided parameters. Each row in the data frame represents a unique combination of the parameters.
 #' 
@@ -5734,6 +5736,7 @@ interpret_simlr_vector <- function( simlrResult, simlrMats, simlrVariable, n2sho
 #' @return A list of ggplot objects.
 #'
 #' @examples
+#' \dontrun{
 #' # Simulate data
 #' set.seed(123)
 #' feature_names <- paste("Feature", 1:10)
@@ -5753,6 +5756,7 @@ interpret_simlr_vector <- function( simlrResult, simlrMats, simlrVariable, n2sho
 #' for (i in 1:length(plots)) {
 #'   print(plots[[i]])
 #' }
+#' }
 #' @export
 plot_features <- function(data_list, take_abs = TRUE, n_limit = 12 ) {
   plots <- list()
diff --git a/man/plot_features.Rd b/man/plot_features.Rd
index f4e60db4..088e4a42 100644
--- a/man/plot_features.Rd
+++ b/man/plot_features.Rd
@@ -20,6 +20,7 @@ A list of ggplot objects.
 Create bar plots for each column in each data frame, showing only non-zero values.  Normalize each feature s.t. max is one.
 }
 \examples{
+\dontrun{
 # Simulate data
 set.seed(123)
 feature_names <- paste("Feature", 1:10)
@@ -40,3 +41,4 @@ for (i in 1:length(plots)) {
   print(plots[[i]])
 }
 }
+}
diff --git a/man/simlr.parameters.Rd b/man/simlr.parameters.Rd
index 1d40ef39..83ee5913 100644
--- a/man/simlr.parameters.Rd
+++ b/man/simlr.parameters.Rd
@@ -36,6 +36,10 @@ simlr.parameters(
 \item{optimus_options}{A list of options for the `optimus` parameter.}
 
 \item{constraint_options}{A list of options for the `constraint` parameter, default is `list("none")`.}
+
+\item{num_samples}{if not full, then the size of the subset space}
+
+\item{search_type}{string vector either full random or deterministic}
 }
 \value{
 A list containing all (or a subset of) combinations of the provided parameters. Each row in the data frame represents a unique combination of the parameters.