From d504136d027b21ba3e6658f43c062e49edc6e5ea Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Thu, 2 Nov 2023 12:05:06 -0400
Subject: [PATCH] Fix roxygen for some functions. Inherit parameters in a
 couple cases instead of just copying

---
 R/multi_gene.R                       | 24 ++++++++-------------
 man/dot-multi_gene_validity_check.Rd | 32 ++++++++++++++++++++++++++++
 2 files changed, 41 insertions(+), 15 deletions(-)
 create mode 100644 man/dot-multi_gene_validity_check.Rd

diff --git a/R/multi_gene.R b/R/multi_gene.R
index 369a11a..92f4e77 100644
--- a/R/multi_gene.R
+++ b/R/multi_gene.R
@@ -23,7 +23,7 @@
 #'
 #' @export
 #' @author Nicholas J. Eagles
-#' @import SpatialExperiment SummarizedExperiment rlang
+#' @import SpatialExperiment SummarizedExperiment
 #' @family Spot plots summarizing expression of multiple genes simultaneously
 #' 
 #' @examples 
@@ -76,24 +76,14 @@ spot_plot_z_score = function(
 #' computed of how many \code{genes} have nonzero expression, and this quantity
 #' is plotted across the entire capture area.
 #'
-#' @param spe A \code{SpatialExperiment} with colData column \code{exclude_overlapping},
-#' passed to \code{spatialLIBD::vis_gene} or \code{spatialLIBD::vis_clus}
-#' @param genes character() of gene names to plot in combination, expected to be
-#' in \code{rownames(spe)}
-#' @param sample_id character(1) passed to \code{sampleid} in
-#' \code{spatialLIBD::vis_gene} or \code{spatialLIBD::vis_clus}. Assumed to be a
-#' donor, possibly consisting of several capture areas to plot at once
-#' @param assayname character(1) passed to \code{spatialLIBD::vis_gene}
-#' @param minCount numeric(1) passed to passed to \code{spatialLIBD::vis_gene}
-#' @param ... Parameters accepted by \code{spot_plot}, excluding
-#' \code{is_discrete} or \code{var_name}, which are handled internally
+#' @inheritParams spot_plot_z_score
 #' 
 #' @return A \code{ggplot} object containing a "spot plot" of the specified
 #' sample and genes
 #'
 #' @export
 #' @author Nicholas J. Eagles
-#' @import SpatialExperiment SummarizedExperiment rlang
+#' @import SpatialExperiment SummarizedExperiment
 #' @family Spot plots summarizing expression of multiple genes simultaneously
 #' 
 #' @examples 
@@ -136,8 +126,12 @@ spot_plot_sparsity = function(
     return(p)
 }
 
-#   Check the validity of arguments passed to plotting functions defined in
-#   this script
+#'   Check the validity of arguments passed to \code{multi_gene.R} plotting functions
+#'
+#' @author Nicholas J. Eagles
+#' @inheritParams spot_plot_z_score
+#' @import SpatialExperiment SummarizedExperiment rlang
+#' @return NULL
 .multi_gene_validity_check = function(
         spe, genes, sample_id, assayname, minCount, ...
     ) {
diff --git a/man/dot-multi_gene_validity_check.Rd b/man/dot-multi_gene_validity_check.Rd
new file mode 100644
index 0000000..851de62
--- /dev/null
+++ b/man/dot-multi_gene_validity_check.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/multi_gene.R
+\name{.multi_gene_validity_check}
+\alias{.multi_gene_validity_check}
+\title{Check the validity of arguments passed to \code{multi_gene.R} plotting functions}
+\usage{
+.multi_gene_validity_check(spe, genes, sample_id, assayname, minCount, ...)
+}
+\arguments{
+\item{spe}{A \code{SpatialExperiment} with colData column \code{exclude_overlapping},
+passed to \code{spatialLIBD::vis_gene} or \code{spatialLIBD::vis_clus}}
+
+\item{genes}{character() of gene names to plot in combination, expected to be
+in \code{rownames(spe)}}
+
+\item{sample_id}{character(1) passed to \code{sampleid} in
+\code{spatialLIBD::vis_gene} or \code{spatialLIBD::vis_clus}. Assumed to be a
+donor, possibly consisting of several capture areas to plot at once}
+
+\item{assayname}{character(1) passed to \code{spatialLIBD::vis_gene}}
+
+\item{minCount}{numeric(1) passed to passed to \code{spatialLIBD::vis_gene}}
+
+\item{...}{Parameters accepted by \code{spot_plot}, excluding
+\code{is_discrete} or \code{var_name}, which are handled internally}
+}
+\description{
+Check the validity of arguments passed to \code{multi_gene.R} plotting functions
+}
+\author{
+Nicholas J. Eagles
+}