scripts: Add input dataset comparison

scripts/datasets.R

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+library(data.table)
+library(here)
+
+i_am("scripts/gsea_vs_cmap.R")
+
+ranking_gtex_all <- ubigen::rank_genes(ubigen::gtex_all)
+ranking_gtex_tissues <- ubigen::rank_genes(ubigen::gtex_tissues)
+ranking_hpa <- ubigen::rank_genes(ubigen::hpa_tissues)
+ranking_cmap <- ubigen::rank_genes(ubigen::cmap)
+
+cor_ranking <- function(ranking_x, ranking_y) {
+  data <- merge(ranking_x, ranking_y, by = "gene")
+
+  stats::cor(
+    data$score.x,
+    data$score.y,
+  ) |>
+    round(digits = 4) |>
+    format(nsmall = 4)
+}
+
+cat("Ranking correlations:")
+cat("\nGTEx (tissues) ~ GTEx (all): ")
+cat(cor_ranking(ranking_gtex_all, ranking_gtex_tissues))
+cat("\nHPA ~ GTEx (all): ")
+cat(cor_ranking(ranking_gtex_all, ranking_hpa))
+cat("\nCMap ~ GTEx (all): ")
+cat(cor_ranking(ranking_gtex_all, ranking_cmap))
+cat("\nCMap ~ GTEx (tissues): ")
+cat(cor_ranking(ranking_gtex_tissues, ranking_cmap))
+cat("\nHPA ~ GTEx (tissues): ")
+cat(cor_ranking(ranking_gtex_tissues, ranking_hpa))
+cat("\nCMap ~ HPA: ")
+cat(cor_ranking(ranking_hpa, ranking_cmap))
+
+# Sample rankings for plots
+
+sample_ranking <- function(ranking) {
+  ranking <- ranking[percentile >= 0.8]
+  ranking[sample(nrow(ranking), 500)]
+}
+
+fig <- plotly::plot_ly() |>
+  plotly::add_lines(
+    data = ranking_gtex_tissues |> sample_ranking(),
+    x = ~percentile,
+    y = ~score,
+    name = "GTEx (tissues)",
+    line = list(
+      color = "#2275d4",
+      width = 4
+    )
+  ) |>
+  plotly::add_lines(
+    data = ranking_hpa |> sample_ranking(),
+    x = ~percentile,
+    y = ~score,
+    name = "HPA (tissues)",
+    line = list(
+      color = "#30c422",
+      width = 4
+    )
+  ) |>
+  plotly::add_lines(
+    data = ranking_cmap |> sample_ranking(),
+    x = ~percentile,
+    y = ~score,
+    name = "CMap (drugs)",
+    line = list(
+      color = "#ff7f2a",
+      width = 4
+    )
+  ) |>
+  plotly::add_lines(
+    data = ranking_gtex_all |> sample_ranking(),
+    x = ~percentile,
+    y = ~score,
+    name = "GTEx (all)",
+    line = list(
+      color = "#7d19bf",
+      width = 4
+    )
+  ) |>
+  plotly::layout(
+    xaxis = list(
+      title = "Percentile",
+      tickformat = ".1%",
+      range = c(0.8, 1)
+    ),
+    yaxis = list(
+      title = "Score",
+      range = c(0, 1)
+    ),
+    font = list(size = 8),
+    margin = list(
+      pad = 2,
+      l = 36,
+      r = 0,
+      t = 0,
+      b = 36
+    ),
+    showlegend = FALSE
+  )
+
+plotly::save_image(
+  fig,
+  file = here("scripts/output/datasets.svg"),
+  width = 6.27 * 72,
+  height = 3.135 * 72,
+  scale = 96 / 72
+)
+
+plotly::save_image(
+  fig |> plotly::layout(showlegend = TRUE),
+  file = here("scripts/output/datasets_legend.svg"),
+  width = 6.27 * 72,
+  height = 3.135 * 72,
+  scale = 96 / 72
+)