Convert to R package

R/rank_plot.R

@@ -0,0 +1,53 @@
+# Draw a plot displaying the rank of reference genes.
+#
+# The input table should contain the following columns:
+#
+#  - `gene` Gene IDs of genes to display.
+#  - `name` Name of genes to display.
+#  - `score` Score of the genes.
+#  - `rank` Rank of the genes based on the score.
+#
+# @param results Results to display.
+# @param reference_gene_ids IDs of reference genes.
+# @param cutoff Cut-off score.
+rank_plot <- function(results, reference_gene_ids, cutoff) {
+    first_not_included_rank <- results[score < cutoff, min(rank)]
+    last_rank <- results[, .N]
+
+    plot <- plotly::plot_ly() |> plotly::add_trace(
+        data = results,
+        x = ~rank,
+        y = ~score,
+        name = "All genes",
+        type = "scatter",
+        mode = "line",
+        hoverinfo = "skip"
+    ) |> plotly::add_trace(
+        data = results[gene %chin% reference_gene_ids],
+        x = ~rank,
+        y = ~score,
+        color = ~gene,
+        name = ~name,
+        width = 10,
+        type = "bar"
+    )  |> plotly::layout(
+        xaxis = list(title = "Ranks"),
+        yaxis = list(title = "Score")
+    )
+
+    if (first_not_included_rank <= last_rank) {
+        plot <- plot |> plotly::layout(
+            shapes = list(
+                type = "rect",
+                fillcolor = "black",
+                opacity = 0.1,
+                x0 = first_not_included_rank,
+                x1 = last_rank,
+                y0 = 0.0,
+                y1 = 1.0
+            )
+        )
+    }
+
+    plot
+}