From 2f24812c903040aece28550a96286a5f5cef3f53 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Wed, 30 Nov 2022 15:27:00 +0100
Subject: [PATCH] Export plot functions

---
 NAMESPACE            |  3 +++
 R/plots.R            |  9 ++++++---
 man/box_plot.Rd      | 19 +++++++++++++++++++
 man/overview_plot.Rd | 21 +++++++++++++++++++++
 man/scores_plot.Rd   | 22 ++++++++++++++++++++++
 5 files changed, 71 insertions(+), 3 deletions(-)
 create mode 100644 man/box_plot.Rd
 create mode 100644 man/overview_plot.Rd
 create mode 100644 man/scores_plot.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 41009d9..9233be5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
 export(analyze)
+export(box_plot)
+export(overview_plot)
 export(rank_genes)
 export(run_app)
+export(scores_plot)
 import(data.table)
 import(shiny)
diff --git a/R/plots.R b/R/plots.R
index 06f2705..c4d664d 100644
--- a/R/plots.R
+++ b/R/plots.R
@@ -5,7 +5,8 @@
 #' @param sample_proportion Proportion of rows to use as the shown sample.
 #'
 #' @return A `plotly` figure.
-#' @noRd
+#'
+#' @export
 overview_plot <- function(ranked_data,
                           highlighted_genes = NULL,
                           sample_proportion = 0.05) {
@@ -67,7 +68,8 @@ overview_plot <- function(ranked_data,
 #' @param highlighted_genes Genes that will be compared.
 #'
 #' @return A `plotly` figure.
-#' @noRd
+#'
+#' @export
 box_plot <- function(ranked_data, highlighted_genes) {
   data <- data.table::copy(ranked_data)
   data[, group := data.table::fifelse(
@@ -96,7 +98,8 @@ box_plot <- function(ranked_data, highlighted_genes) {
 #'   `NULL`, all ranks will be shown.
 #'
 #' @return A `plotly` figure for rendering.
-#' @noRd
+#' 
+#' @export
 scores_plot <- function(ranked_data, highlighted_genes = NULL, ranks = 1000) {
   data <- if (is.null(ranks)) {
     ranked_data
diff --git a/man/box_plot.Rd b/man/box_plot.Rd
new file mode 100644
index 0000000..0ad6510
--- /dev/null
+++ b/man/box_plot.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{box_plot}
+\alias{box_plot}
+\title{Create a plot comparing some genes with the overall ranking.}
+\usage{
+box_plot(ranked_data, highlighted_genes)
+}
+\arguments{
+\item{ranked_data}{The ranking to visualize.}
+
+\item{highlighted_genes}{Genes that will be compared.}
+}
+\value{
+A \code{plotly} figure.
+}
+\description{
+Create a plot comparing some genes with the overall ranking.
+}
diff --git a/man/overview_plot.Rd b/man/overview_plot.Rd
new file mode 100644
index 0000000..bf3bad8
--- /dev/null
+++ b/man/overview_plot.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{overview_plot}
+\alias{overview_plot}
+\title{Create a plot showing an overview over the provided ranking.}
+\usage{
+overview_plot(ranked_data, highlighted_genes = NULL, sample_proportion = 0.05)
+}
+\arguments{
+\item{ranked_data}{The ranking to visualize.}
+
+\item{highlighted_genes}{Genes that will be marked.}
+
+\item{sample_proportion}{Proportion of rows to use as the shown sample.}
+}
+\value{
+A \code{plotly} figure.
+}
+\description{
+Create a plot showing an overview over the provided ranking.
+}
diff --git a/man/scores_plot.Rd b/man/scores_plot.Rd
new file mode 100644
index 0000000..d484043
--- /dev/null
+++ b/man/scores_plot.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{scores_plot}
+\alias{scores_plot}
+\title{Create plot showing the distribution of scores using \code{plotly}.}
+\usage{
+scores_plot(ranked_data, highlighted_genes = NULL, ranks = 1000)
+}
+\arguments{
+\item{ranked_data}{Data on genes with precomputed ranks.}
+
+\item{highlighted_genes}{Genes that will be marked.}
+
+\item{ranks}{How may ranks the x-axis should include. If this parameter is
+\code{NULL}, all ranks will be shown.}
+}
+\value{
+A \code{plotly} figure for rendering.
+}
+\description{
+Create plot showing the distribution of scores using \code{plotly}.
+}