scripts: Add new comparison plots

scripts/comparison.R

@@ -24,14 +24,114 @@ partitions <- VennDiagram::get.venn.partitions(datasets) |> data.table()
 genes_venn <- partitions[1]$..values..[[1]]
 write(genes_venn, file = here("scripts/output/genes_venn.txt"))
 
+gene_sets <- fread(here("scripts/input/gene_sets.csv"))
+genes_literature <- gene_sets[type == "literature", unique(gene)]
+genes_recommended <- gene_sets[type == "expression", unique(gene)]
+genes_literature_ids <- data.table(
+  gene = genes_literature,
+  literature_id = seq_along(genes_literature)
+)
+
 ranking_gtex <- ubigen::rank_genes(ubigen::gtex_all)
 ranking_cmap <- ubigen::rank_genes(ubigen::cmap)
 
-data <- merge(
+data <- fread(here("scripts/output/gsea_vs_cmap_groups.csv"))
-  ranking_gtex[, .(gene, score, percentile)],
+
-  ranking_cmap[, .(gene, score, percentile)],
+genes_table <- gene_sets[type == "literature"]
-  by = "gene",
+genes_table[, hgnc_symbol := gprofiler2::gconvert(gene, target = "HGNC")$target]
-  suffixes = c(x = "_gtex", y = "_cmap")
+genes_table <- genes_table[,
+  .(
+    gene = unique(gene),
+    source = paste(label, collapse = ", ")
+  ),
+  by = hgnc_symbol
+]
+genes_table <- merge(genes_table, data, by = "gene", sort = FALSE)
+fwrite(genes_table, file = here("scripts/output/genes_table.csv"))
+
+datasets_data <- rbindlist(lapply(names(datasets), function(name) {
+  data.table(
+    dataset = name,
+    gene = datasets[[name]]
+  )
+}))
+
+datasets_data <- rbind(
+  datasets_data,
+  data.table(
+    dataset = "Venn",
+    gene = genes_venn
+  )
+)
+
+datasets_data <- rbind(
+  datasets_data,
+  data.table(
+    dataset = "Recommended",
+    gene = genes_recommended
+  )
+)
+
+datasets_data <- rbind(
+  datasets_data,
+  data.table(
+    dataset = "Literature",
+    gene = genes_literature
+  )
+)
+
+datasets_data <- merge(datasets_data, data, by = "gene")
+
+datasets_table <- datasets_data[, .(count = .N), by = c("dataset", "group")]
+datasets_table[, total := sum(count), by = dataset]
+datasets_table[, proportion := count / total]
+
+group_plots <- list()
+
+for (group_value in datasets_table[, unique(group)]) {
+  group_plot <- plotly::plot_ly() |>
+    plotly::add_bars(
+      data = datasets_table[group == group_value],
+      x = ~dataset,
+      color = ~dataset,
+      y = ~proportion
+    ) |>
+    plotly::layout(
+      xaxis = list(
+        categoryarray = datasets_table[, unique(dataset)],
+        title = ""
+      ),
+      yaxis = list(
+        range = c(0.0, 1.0),
+        title = ""
+      ),
+      font = list(size = 8),
+      margin = list(
+        pad = 2,
+        l = 0,
+        r = 0,
+        t = 0,
+        b = 36
+      )
+    )
+
+  plotly::save_image(
+    group_plot |> plotly::hide_legend(),
+    file = here(glue::glue("scripts/output/gene_sets_{group_value}.svg")),
+    width = 3 * 72,
+    height = 4 * 72,
+    scale = 96 / 72
+  )
+
+  group_plots <- c(group_plots, list(group_plot))
+}
+
+plotly::save_image(
+  group_plot,
+  file = here(glue::glue("scripts/output/gene_sets_legend.svg")),
+  width = 6.27 * 72,
+  height = 6.27 * 72,
+  scale = 96 / 72
 )
 
 data[, count := 0]
@@ -45,7 +145,7 @@ threshold_cmap <- data[percentile_cmap >= 0.95, min(score_cmap)]
 
 fig <- plotly::plot_ly() |>
   plotly::add_markers(
-    data = data[count >= 1],
+    data = data[count >= 1 & !(gene %chin% genes_literature)],
     x = ~score_gtex,
     y = ~score_cmap,
     color = ~count,
@@ -56,6 +156,19 @@ fig <- plotly::plot_ly() |>
     ),
     cliponaxis = FALSE
   ) |>
+  plotly::add_text(
+    data = merge(
+      data[gene %chin% genes_literature],
+      genes_literature_ids
+    ),
+    x = ~score_gtex,
+    y = ~score_cmap,
+    text = ~ as.character(literature_id),
+    textfont = list(
+      size = 8,
+      color = "green"
+    )
+  ) |>
   plotly::layout(
     xaxis = list(
       title = "Ranking based on GTEx",