Start adding an UI using Shiny

scatter_plot.R

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+library(data.table)
+library(ggplot2)
+
+#' Draw a scatter plot containing gene positions.
+scatter_plot <- function(gene_ids, data) {
+    species <- data$species
+    setorder(species, median_distance)
+
+    distances <- data$distances[geneid %in% gene_ids]
+
+    plot <- ggplot() +
+        scale_x_continuous(
+            name = "Species",
+            breaks = seq_len(nrow(species)),
+            labels = species$label
+        ) +
+        scale_y_continuous(name = "Distance to telomeres [Mbp]") +
+        geom_line(
+            species,
+            mapping = aes(
+                x = as.numeric(rownames(species)),
+                y = median_distance / 1000000
+            )
+        )
+
+    colors <- rainbow(length(gene_ids))
+
+    for (i in seq_len(length(gene_ids))) {
+        gene_id <- gene_ids[i]
+
+        gene_distances <- data.table(
+            index = as.numeric(rownames(species)),
+            distance = unlist(distances[geneid == gene_id, -1])
+        )
+
+        plot <- plot +
+            geom_point(
+                gene_distances,
+                mapping = aes(
+                    x = index,
+                    y = distance / 1000000,
+                ),
+                color = colors[i]
+            )
+    }
+
+    plot
+    
+    # plot(
+    #     species[, median_distance] / 1000000,
+    #     type = "l",
+    #     xaxt = "n",
+    #     xlab = "",
+    #     ylab = "Distance to telomere (Mbp)",
+    #     bty = "n"
+    # )
+
+    # axis(
+    #     1,
+    #     at = seq_len(nrow(species)),
+    #     tick = FALSE,
+    #     labels = FALSE
+    # )
+
+    # mtext(
+    #     data$species[, label],
+    #     side = 1,
+    #     at = seq_len(nrow(species)),
+    #     las = 2,
+    #     # col = axis.labels.col,
+    #     adj = 1
+    # )
+}