From a67804949dfd2f4141cd450b1b401a2bd55658af Mon Sep 17 00:00:00 2001
From: Michael Geuenich <m.geuenich@mail.utoronto.ca>
Date: Thu, 1 Jun 2023 21:59:55 -0700
Subject: [PATCH] AR params

---
 pipeline/figures/AR-params.R | 61 ++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 pipeline/figures/AR-params.R

diff --git a/pipeline/figures/AR-params.R b/pipeline/figures/AR-params.R
new file mode 100644
index 0000000..0492b13
--- /dev/null
+++ b/pipeline/figures/AR-params.R
@@ -0,0 +1,61 @@
+suppressPackageStartupMessages(
+  library(tidyverse)
+)
+source("pipeline/whatsthatcell-helpers.R")
+
+
+cytof_acc <- read_tsv("output/v7/results/overall-CyTOF-benchmarking-accuracies.tsv") |> 
+  mutate(cohort = "CyTOF")
+scrna_acc <- read_tsv("output/v7/results/overall-scRNASeq-benchmarking-accuracies.tsv") |> 
+  mutate(cohort = "scRNASeq")
+snrna_acc <- read_tsv("output/v7/results/overall-snRNASeq-benchmarking-accuracies.tsv") |> 
+  mutate(cohort = "snRNASeq")
+
+acc <- bind_rows(cytof_acc, scrna_acc, snrna_acc)
+
+
+
+plot_knn_res <- function(acc, fill, cohort){
+  acc <- filter(acc, selection_procedure == "MarkerSeurat_clustering" |
+                  selection_procedure == "NoMarkerSeurat_clustering") |> 
+    mutate(selection_procedure = case_when(selection_procedure == "MarkerSeurat_clustering" ~ "AR Marker",
+                                           selection_procedure == "NoMarkerSeurat_clustering" ~ "AR No Marker")) |> 
+    filter(.metric == "f_meas")
+  
+  if(fill == "res"){
+    acc |>
+      ggplot(aes(x = as.character(cell_num), y = .estimate, fill = as.character(res))) +
+      geom_boxplot() +
+      labs(x = "Number of cells", y = "F1 score", fill = "Clustering\nresolution",
+           title = cohort) +
+      facet_grid(method ~ selection_procedure + knn) +
+      whatsthatcell_theme()
+  }else if(fill == "knn"){
+    acc |> 
+      ggplot(aes(x = as.character(cell_num), y = .estimate, fill = as.character(knn))) +
+      geom_boxplot() +
+      labs(x = "Number of cells", y = "F1 score", fill = "Number of\nnearest\nneighbours",
+           title = cohort) +
+      facet_grid(method ~ selection_procedure + res) +
+      whatsthatcell_theme()
+  }
+}
+
+
+pdf("output/v7/paper-figures/supp-AR-res.pdf", height = 14, width = 9)
+  (plot_knn_res(cytof_acc, "res", "CyTOF") /
+    plot_knn_res(scrna_acc, "res", "scRNASeq") /
+    plot_knn_res(snrna_acc, "res", "snRNASeq")) +
+    plot_layout(guides = "collect", heights = c(1, 2, 2))
+dev.off()
+
+
+pdf("output/v7/paper-figures/supp-AR-knn.pdf", height = 14, width = 9)
+(plot_knn_res(cytof_acc, "knn", "CyTOF") /
+    plot_knn_res(scrna_acc, "knn", "scRNASeq") /
+    plot_knn_res(snrna_acc, "knn", "snRNASeq")) +
+  plot_layout(guides = "collect", heights = c(1, 2, 2))
+dev.off()
+
+
+