misc: a script for miscellaneous plots (for presentations, grants, etc.)

src/90_34_random-description-plots.R

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+# A file for making a few miscellaneous plots for presentations, etc.
+
+GRAPHS_DIR <- "90_34_random-description-plots"
+reset_graph_directory(GRAPHS_DIR)
+
+
+
+#### ---- DepMap value distribution ---- ####
+
+depmap_dist_plot_data <- depmap_modelling_df %>%
+    filter(cancer == "PAAD") %>%
+    group_by(hugo_symbol) %>%
+    summarize(gene_effect = median(gene_effect, na.rm = TRUE)) %>%
+    ungroup()
+
+depmap_dist_plot_data2 <- depmap_dist_plot_data %>%
+    inner_join(
+        essentiality_tib %>%
+            select(hugo_symbol, label) %>%
+            filter(label %in% c("achilles_essential", "nonessential")) %>%
+            group_by(hugo_symbol) %>%
+            filter(n() == 1 | label == "nonessential") %>%
+            ungroup(),
+        by = "hugo_symbol"
+    ) %>%
+    mutate(label = case_when(
+        label == "achilles_essential" ~ "essential genes",
+        label == "nonessential" ~ "nonessential genes",
+        TRUE ~ NA_character_
+    ))
+
+
+essential_pal <- c(
+    "essential genes" = "#1B9E77",
+    "nonessential genes" = "#D95F02"
+)
+
+
+depmap_dist_plot <- depmap_dist_plot_data %>%
+    ggplot(aes(x = gene_effect)) +
+    geom_vline(xintercept = c(0, -1), lty = 2, color = "grey50", size = 1) +
+    geom_density(aes(color = label, fill = label), alpha = 0.5, size = 0,
+                 data = depmap_dist_plot_data2) +
+    geom_density(color = "grey20", fill = NA, size = 1.1) +
+    annotate("text",
+             label = names(essential_pal), color = essential_pal,
+             x = c(-2, -0.5),
+             y = c(0.6, 2.5),
+             family = "Arial", size = 6, fontface = "bold"
+         ) +
+    scale_x_continuous(limits = c(NA, 0.5)) +
+    scale_y_continuous(expand = expansion(mult = c(0, 0.02))) +
+    scale_fill_manual(values = essential_pal, guide = FALSE) +
+    scale_color_manual(values = essential_pal, guide = FALSE) +
+    theme_minimal(base_size  = 14, base_family = "Arial") +
+    theme(
+        legend.position = c(0.1, 0.2),
+        legend.title = element_blank()
+    ) +
+    labs(x = "median dependency score per gene",
+         y = "density")
+ggsave_wrapper(
+    depmap_dist_plot,
+    plot_path(GRAPHS_DIR, "depmap-dist-plot.jpeg"),
+    "wide"
+)
+
+