plots: Move rank plot and add boxplot

NAMESPACE

@@ -1,11 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(plot,geposan_ranking)
 S3method(print,geposan_comparison)
 S3method(print,geposan_preset)
 export(analyze)
 export(compare)
 export(optimal_weights)
+export(plot_boxplot)
+export(plot_scores)
 export(preset)
 export(ranking)
 import(data.table)

R/plots.R

@@ -0,0 +1,95 @@
+#' Plot a ranking as a scatter plot of scores.
+#'
+#' This function requires the package `plotly`.
+#'
+#' @param ranking The ranking to visualize.
+#' @param gene_sets A list of gene sets (containing vectors of gene IDs) that
+#'   will be highlighted in the plot.
+#' @param labels Labels for the gene sets. This is required if gene sets are
+#'   given and has to have the same length.
+#'
+#' @seealso ranking()
+#'
+#' @export
+plot_scores <- function(ranking, gene_sets = NULL, labels = NULL) {
+    if (!requireNamespace("plotly", quietly = TRUE)) {
+        stop("Please install \"plotly\" to use this function.")
+    }
+
+    plot <- plotly::plot_ly() |>
+        plotly::add_trace(
+            data = ranking,
+            x = ~rank,
+            y = ~score,
+            color = "All genes",
+            type = "scatter",
+            mode = "markers",
+            hoverinfo = "skip"
+        ) |>
+        plotly::layout(
+            xaxis = list(title = "Rank"),
+            yaxis = list(title = "Score")
+        )
+
+    if (length(gene_sets) > 0) {
+        # Take out the genes to be highlighted.
+        gene_set_data <- ranking[gene %chin% unlist(gene_sets)]
+
+        # Add labels for each gene set.
+        for (i in seq_along(gene_sets)) {
+            gene_set_data[gene %chin% gene_sets[[i]], label := labels[i]]
+        }
+
+        # Include gene information which will be used for labeling
+        gene_set_data <- merge(gene_set_data, genes, by.x = "gene", by.y = "id")
+
+        plot <- plot |> plotly::add_trace(
+            data = gene_set_data,
+            x = ~rank,
+            y = ~score,
+            color = ~label,
+            text = ~name,
+            type = "scatter",
+            mode = "markers",
+            marker = list(size = 20)
+        )
+    }
+
+    plot
+}
+
+#' Visualize a ranking by comparing gene sets in a boxplot.
+#'
+#' This function requires the package `plotly`.
+#'
+#' @param ranking The ranking to visualize.
+#' @param gene_sets A list of gene sets (containing vectors of gene IDs) that
+#'   will be shown as separate boxes.
+#' @param labels Labels for the gene sets. This is required if gene sets are
+#'   given and has to have the same length.
+#'
+#' @seealso ranking()
+#'
+#' @export
+plot_boxplot <- function(ranking, gene_sets = NULL, labels = NULL) {
+    if (!requireNamespace("plotly", quietly = TRUE)) {
+        stop("Please install \"plotly\" to use this function.")
+    }
+
+    data <- copy(ranking)
+
+    # Add labels for each gene set.
+    for (i in seq_along(gene_sets)) {
+        data[gene %chin% gene_sets[[i]], label := labels[i]]
+    }
+
+    # Label the other genes.
+    data[!gene %chin% unlist(gene_sets), label := "Other genes"]
+
+    plotly::plot_ly(
+        data = data,
+        y = ~score,
+        color = ~label,
+        type = "box"
+    )
+}

R/ranking.R

@@ -37,62 +37,6 @@ ranking <- function(analysis, weights) {
     )
 }
 
-#' S3 method for plotting a ranking.
-#'
-#' @param gene_sets A list of gene sets (containing vectors of gene IDs) that
-#'   will be highlighted in the plot.
-#' @param labels Labels for the gene sets.
-#'
-#' @seealso ranking()
-#'
-#' @export
-plot.geposan_ranking <- function(ranking, gene_sets = NULL, labels = NULL) {
-    if (!requireNamespace("plotly", quietly = TRUE)) {
-        stop("Please install \"plotly\" to use this function.")
-    }
-
-    plot <- plotly::plot_ly() |>
-        plotly::add_trace(
-            data = ranking,
-            x = ~rank,
-            y = ~score,
-            color = "All genes",
-            type = "scatter",
-            mode = "markers",
-            hoverinfo = "skip"
-        ) |>
-        plotly::layout(
-            xaxis = list(title = "Rank"),
-            yaxis = list(title = "Score")
-        )
-
-    if (length(gene_sets) > 0) {
-        # Take out the genes to be highlighted.
-        gene_set_data <- ranking[gene %chin% unlist(gene_sets)]
-
-        # Add labels for each gene set.
-        for (i in seq_along(gene_sets)) {
-            gene_set_data[gene %chin% gene_sets[[i]], label := labels[i]]
-        }
-
-        # Include gene information which will be used for laebling
-        gene_set_data <- merge(gene_set_data, genes, by.x = "gene", by.y = "id")
-
-        plot <- plot |> plotly::add_trace(
-            data = gene_set_data,
-            x = ~rank,
-            y = ~score,
-            color = ~label,
-            text = ~name,
-            type = "scatter",
-            mode = "markers",
-            marker = list(size = 20)
-        )
-    }
-
-    plot
-}
-
 #' Find the best weights to rank the results.
 #'
 #' This function finds the optimal parameters to [ranking()] that result in the

man/plot.geposan_ranking.Rd

@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ranking.R
-\name{plot.geposan_ranking}
-\alias{plot.geposan_ranking}
-\title{S3 method for plotting a ranking.}
-\usage{
-\method{plot}{geposan_ranking}(ranking, gene_sets = NULL, labels = NULL)
-}
-\arguments{
-\item{gene_sets}{A list of gene sets (containing vectors of gene IDs) that
-will be highlighted in the plot.}
-
-\item{labels}{Labels for the gene sets.}
-}
-\description{
-S3 method for plotting a ranking.
-}
-\seealso{
-ranking()
-}

man/plot_boxplot.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{plot_boxplot}
+\alias{plot_boxplot}
+\title{Visualize a ranking by comparing gene sets in a boxplot.}
+\usage{
+plot_boxplot(ranking, gene_sets = NULL, labels = NULL)
+}
+\arguments{
+\item{ranking}{The ranking to visualize.}
+
+\item{gene_sets}{A list of gene sets (containing vectors of gene IDs) that
+will be shown as separate boxes.}
+
+\item{labels}{Labels for the gene sets. This is required if gene sets are
+given and has to have the same length.}
+}
+\description{
+This function requires the package \code{plotly}.
+}
+\seealso{
+ranking()
+}

man/plot_scores.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{plot_scores}
+\alias{plot_scores}
+\title{Plot a ranking as a scatter plot of scores.}
+\usage{
+plot_scores(ranking, gene_sets = NULL, labels = NULL)
+}
+\arguments{
+\item{ranking}{The ranking to visualize.}
+
+\item{gene_sets}{A list of gene sets (containing vectors of gene IDs) that
+will be highlighted in the plot.}
+
+\item{labels}{Labels for the gene sets. This is required if gene sets are
+given and has to have the same length.}
+}
+\description{
+This function requires the package \code{plotly}.
+}
+\seealso{
+ranking()
+}