add rem cell type

pipeline/figures/rem-cell-type.R

@@ -0,0 +1,188 @@
+suppressPackageStartupMessages({
+  library(tidyverse)
+  library(patchwork)
+})
+source("pipeline/whatsthatcell-helpers.R")
+
+# Read in data
+### scRNASeq
+scrna <- c(
+  list.files("output/v7/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-JIMT1*highest*multi*20*"),
+             full.names = TRUE),
+  list.files("output/v7/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-AU565*highest*multi*20*"),
+             full.names = TRUE),
+  list.files("output/v7/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-JIMT1*highest*rf*20*"),
+             full.names = TRUE),
+  list.files("output/v7/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-AU565*highest*rf*20*"),
+             full.names = TRUE)
+)
+
+scrna <- lapply(scrna, read_tsv) |> 
+  bind_rows() |> 
+  mutate(al = case_when(grepl('rf', params) ~ "rf",
+                        grepl('multinom', params) ~ "multinom"),
+         params = gsub(".*rem_celltype-", "", params),
+         params = gsub("-seed-[0-9]", "", params))
+
+
+scrna_box <- scrna |> 
+  mutate(al = case_when(al == "multinom" ~ "LR",
+                        al == "rf" ~ "RF")) |> 
+  ggplot(aes(x = gt_cell_type, y = criterion_val, 
+             fill = as.character(num_missing_cells))) +
+  geom_boxplot(outlier.colour = "lightgrey", outlier.size = 0.4) +
+  labs(y = "Scaled entropy", x = "Ground truth cell type",
+       fill = "Number of cells of the type removed in dataset") +
+  facet_grid(al ~ params) +
+  whatsthatcell_theme() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))
+
+
+### snRNASeq
+snrna <- c(
+  list.files("output/v7/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-Ductal*highest*multi*20*"),
+             full.names = TRUE),
+  list.files("output/v7/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-Endothelial*highest*multi*20*"),
+             full.names = TRUE),
+  list.files("output/v7/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-Schwann*highest*multi*20*"),
+             full.names = TRUE),
+  list.files("output/v7/results/rem_cell_type_group/",
+             pattern = glob2rx("*random*l1*sn*high*multi*num-20*"),
+             full.names = TRUE)
+)
+
+snrna <- lapply(snrna, read_tsv) |> 
+  bind_rows() |> 
+  mutate(al = case_when(grepl('rf', params) ~ "rf",
+                        grepl('multinom', params) ~ "multinom"),
+         params = gsub(".*rem_celltype-", "", params),
+         params = gsub("-seed-[0-9]", "", params))
+
+snrna_box <- snrna |> 
+  mutate(params = factor(params, levels = c("Ductal", "Endothelial", "Schwann", 
+                                            "Endothelial, Schwann"))) |> 
+  ggplot(aes(x = gt_cell_type, y = criterion_val, 
+             fill = as.character(num_missing_cells))) +
+  geom_boxplot(outlier.colour = "lightgrey", outlier.size = 0.4) +
+  labs(y = "Scaled entropy", x = "Ground truth cell type",
+       fill = "Number of cells of the type removed in dataset") +
+  facet_wrap(~ params) +
+  whatsthatcell_theme() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))
+
+### Cytof
+cytof <- c(
+  list.files("output/v7/results/rem_cell_type",
+             pattern = glob2rx("*random*rem-Classical*CyTOF*highest*multi*20*"),
+             full.names = TRUE),
+  list.files("output/v7/results/rem_cell_type",
+             pattern = glob2rx("*random*CD8*CyTOF*highest*multi*20*"),
+             full.names = TRUE)
+)
+
+
+cytof <- lapply(cytof, read_tsv) |> 
+  bind_rows() |> 
+  mutate(al = case_when(grepl('rf', params) ~ "rf",
+                        grepl('multinom', params) ~ "multinom"),
+         params = gsub(".*rem_celltype-", "", params),
+         params = gsub("-seed-[0-9]", "", params))
+
+cytof_box <- cytof |> 
+  ggplot(aes(x = gt_cell_type, y = criterion_val, 
+             fill = as.character(num_missing_cells))) +
+  geom_boxplot(outlier.colour = "lightgrey", outlier.size = 0.4) +
+  labs(y = "Scaled entropy", x = "Ground truth cell type",
+       fill = "Number of cells of the type removed in dataset") +
+  facet_wrap(~ params, ncol = 1) +
+  whatsthatcell_theme() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))
+
+
+## Combine
+pdf("output/v8/paper-figures/rem-cell-type.pdf", height = 6, width = 14)
+(scrna_box | snrna_box | cytof_box) +
+  plot_layout(guides = "collect", widths = c(2, 2, 1)) +
+  plot_annotation(tag_levels = "A") & 
+  theme(legend.position = 'bottom', plot.tag = element_text(size = 18))
+dev.off()
+
+
+
+## Supplemental for RF for snRNASeq and CyTOF
+snrna_sup <- c(
+  list.files("output/v8/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-Ductal*highest*rf*20*"),
+             full.names = TRUE),
+  list.files("output/v8/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-Endothelial*highest*rf*20*"),
+             full.names = TRUE),
+  list.files("output/v8/results/rem_cell_type/", 
+             pattern = glob2rx("Init-sel-random-rem-Schwann*highest*rf*20*"),
+             full.names = TRUE),
+  list.files("output/v8/results/rem_cell_type_group/",
+             pattern = glob2rx("*random*l1*sn*high*rf*num-20*"),
+             full.names = TRUE)
+)
+
+snrna_sup <- lapply(snrna_sup, read_tsv) |> 
+  bind_rows() |> 
+  mutate(al = case_when(grepl('rf', params) ~ "rf",
+                        grepl('multinom', params) ~ "multinom"),
+         params = gsub(".*rem_celltype-", "", params),
+         params = gsub("-seed-[0-9]", "", params))
+
+cytof_sup <- c(
+  list.files("output/v8/results/rem_cell_type",
+             pattern = glob2rx("*random*rem-Classical*CyTOF*highest*rf*20*"),
+             full.names = TRUE),
+  list.files("output/v8/results/rem_cell_type",
+             pattern = glob2rx("*random*CD8*CyTOF*highest*rf*20*"),
+             full.names = TRUE)
+)
+
+
+cytof_sup <- lapply(cytof_sup, read_tsv) |> 
+  bind_rows() |> 
+  mutate(al = case_when(grepl('rf', params) ~ "rf",
+                        grepl('multinom', params) ~ "multinom"),
+         params = gsub(".*rem_celltype-", "", params),
+         params = gsub("-seed-[0-9]", "", params))
+
+
+snrna_sup_box <- snrna_sup |> 
+  mutate(params = factor(params, levels = c("Ductal", "Endothelial", "Schwann", 
+                                            "Endothelial, Schwann"))) |> 
+  ggplot(aes(x = gt_cell_type, y = criterion_val, 
+             fill = as.character(num_missing_cells))) +
+  geom_boxplot(outlier.colour = "lightgrey", outlier.size = 0.4) +
+  labs(y = "Scaled entropy", x = "Ground truth cell type",
+       fill = "Number of cells of the type removed in dataset") +
+  facet_wrap(~ params) +
+  whatsthatcell_theme() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))
+
+
+
+cytof_sup_box <- cytof_sup |> 
+  ggplot(aes(x = gt_cell_type, y = criterion_val, 
+             fill = as.character(num_missing_cells))) +
+  geom_boxplot(outlier.colour = "lightgrey", outlier.size = 0.4) +
+  labs(y = "Scaled entropy", x = "Ground truth cell type",
+       fill = "Number of cells of the type removed in dataset") +
+  facet_wrap(~ params, ncol = 1) +
+  whatsthatcell_theme() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))
+
+pdf("output/v8/paper-figures/supp-rem-cell-type.pdf", height = 6, width = 10)
+  (snrna_sup_box | cytof_sup_box) +
+    plot_layout(guides = "collect", widths = c(2, 1)) +
+    plot_annotation(tag_levels = "A") & theme(legend.position = 'bottom')
+dev.off()