scripts: Add comparison to other datasets

scripts/comparison.R

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+library(data.table)
+library(here)
+
+i_am("scripts/comparison.R")
+
+w2000 <- scan(here("scripts/input/datasets/warrington_2000.txt"), character())
+z2008 <- scan(here("scripts/input/datasets/zhu_2008.txt"), character())
+e2013 <- scan(here("scripts/input/datasets/eisenberg_2013.txt"), character())
+c2011 <- scan(here("scripts/input/datasets/chang_2011.txt"), character())
+j2022 <- scan(here("scripts/input/datasets/joshi_2022.txt"), character())
+
+datasets <- list(
+  "Warrington 2000" = w2000,
+  "Zhu 2008" = z2008,
+  "Eisenberg 2013" = e2013,
+  "Chang 2011" = c2011,
+  "Joshi 2022" = j2022
+)
+
+ranking_gtex <- ubigen::rank_genes(ubigen::gtex_all)
+ranking_cmap <- ubigen::rank_genes(ubigen::cmap)
+
+data <- merge(
+  ranking_gtex[, .(gene, score, percentile)],
+  ranking_cmap[, .(gene, score, percentile)],
+  by = "gene",
+  suffixes = c(x = "_gtex", y = "_cmap")
+)
+
+data[, count := 0]
+
+for (dataset in datasets) {
+  data[gene %chin% dataset, count := count + 1]
+}
+
+threshold_gtex <- data[percentile_gtex >= 0.95, min(score_gtex)]
+threshold_cmap <- data[percentile_cmap >= 0.95, min(score_cmap)]
+
+fig <- plotly::plot_ly() |>
+  plotly::add_markers(
+    data = data,
+    x = ~score_gtex,
+    y = ~score_cmap,
+    color = ~count,
+    colors = c("#7d19bf", "#ff7f2a"),
+    marker = list(
+      size = 4,
+      opacity = 0.8
+    ),
+    cliponaxis = FALSE
+  ) |>
+  plotly::layout(
+    xaxis = list(
+      title = "Ranking based on GTEx",
+      range = c(0, 1)
+    ),
+    yaxis = list(
+      title = "Ranking based on CMap",
+      range = c(0, 1)
+    ),
+    annotations = list(
+      list(
+        text = "95%",
+        x = threshold_gtex,
+        y = 1,
+        xshift = 2,
+        yshift = 3,
+        yref = "paper",
+        xanchor = "left",
+        yanchor = "top",
+        showarrow = FALSE
+      ),
+      list(
+        text = "95%",
+        x = 1,
+        y = threshold_cmap,
+        yshift = 2,
+        xref = "paper",
+        xanchor = "right",
+        yanchor = "bottom",
+        showarrow = FALSE
+      )
+    ),
+    shapes = list(
+      list(
+        type = "line",
+        y0 = 0,
+        y1 = 1,
+        yref = "paper",
+        x0 = threshold_gtex,
+        x1 = threshold_gtex,
+        line = list(
+          color = "#00000080",
+          opacity = 0.5,
+          width = 1,
+          dash = "dot"
+        )
+      ),
+      list(
+        type = "line",
+        y0 = threshold_cmap,
+        y1 = threshold_cmap,
+        x0 = 0,
+        x1 = 1,
+        xref = "paper",
+        line = list(
+          color = "#00000080",
+          width = 1,
+          opacity = 0.5,
+          dash = "dot"
+        )
+      )
+    ),
+    font = list(size = 8),
+    margin = list(
+      pad = 2,
+      l = 36,
+      r = 0,
+      t = 0,
+      b = 36
+    )
+  ) |>
+  plotly::hide_legend() |>
+  plotly::hide_colorbar()
+
+plotly::save_image(
+  fig,
+  file = here("scripts/output/comparison.svg"),
+  width = 6.27 * 72,
+  height = 6.27 * 72,
+  scale = 96 / 72
+)