Update final figures

code/manuscript-figures.R

 library(ggplot2)
 library(patchwork)
+library(dplyr)
+
+source(here::here("code", "plot-utils.R"))
 
 label_pars <- c(
   "scanpy_wilcoxontiecorrect_rankby_abs",
@@ -125,7 +128,7 @@ ggsave(
   filename = here::here("figures", "final", "concordance-figure.pdf"),
   plot = concordance_figure,
   width = 16,
-  height = 16,
+  height = 18,
   units = "in"
 )
 
@@ -185,7 +188,7 @@ simulated_perf_figure
 ggsave(
   filename = here::here("figures", "final", "simulated-perf-figure.pdf"),
   plot = simulated_perf_figure,
-  width = 12,
+  width = 14,
   height = 8,
   units = "in"
 )
@@ -233,7 +236,7 @@ zhao_pred_perf <- readRDS(
 )
 
 overall_multiclass_pred_plot <- readRDS(
-  here::here("figures", "raw", "overall-mc-pred-plot.rds")
+  here::here("figures", "raw", "overall-mc-pred-plot-z-score-knn.rds")
 )
 
 pbmc3k_seurat_wilcox_confmat <- readRDS(
@@ -290,6 +293,24 @@ ggsave(
   units = "in"
 )
 
+# Poster case studies figure
+
+poster_case_studies_figure <- scanpy_seurat_zeisel_oligodendrocytes_plot +
+  log_fc_plot +
+  plot_layout(ncol = 2) +
+  plot_annotation(tag_levels = "a") &
+  theme(plot.tag = element_text(size = 18))
+
+poster_case_studies_figure
+
+ggsave(
+  filename = here::here("figures", "final", "poster-case-studies-figure.pdf"),
+  plot = poster_case_studies_figure,
+  width = 14,
+  height = 8,
+  units = "in"
+)
+
 # Supplementary figures
 
 # Additional expert heatmaps
@@ -309,8 +330,8 @@ ss3_pbmc_zeisel_expert_heatmaps <- expert_ss3_pbmc3_heatmap + expert_zeisel_heat
 ggsave(
   here::here("figures", "final", "ss3_pbmc-zeisel-expert-heatmaps.pdf"),
   ss3_pbmc_zeisel_expert_heatmaps,
-  width = 12,
-  height = 8,
+  width = 16,
+  height = 12,
   units = "in"
 )
 
@@ -319,8 +340,7 @@ ggsave(
 expert_ss3_pbmc_n_annotated <- readRDS(
   here::here("figures", "raw", "expert-ss3_pbmc-n-annotated.rds")
 ) +
-  theme(legend.position = "none") +
-  ggtitle("SS3 data (At most 5 genes selected)")
+  theme(legend.position = "none")
 
 expert_zeisel_n_annotated <- readRDS(
   here::here("figures", "raw", "expert-zeisel-n-annotated.rds")
@@ -336,8 +356,8 @@ ss3_pbmc_zeisel_expert_n_annotated
 ggsave(
   here::here("figures", "final", "ss3_pbmc-zeisel-expert-n-annotated.pdf"),
   ss3_pbmc_zeisel_expert_n_annotated,
-  width = 12,
-  height = 8,
+  width = 16,
+  height = 12,
   units = "in"
 )
 
@@ -380,3 +400,27 @@ ggsave(
   units = "in"
 )
 
+# SVM
+
+svm_overall_pred_perf <- readRDS(
+  here::here("figures", "raw", "overall-mc-pred-plot-z-score-svm.rds")
+)
+
+svm_zhao <- readRDS(
+  here::here("figures", "raw", "zhao-pred-perf-svm.rds")
+)
+
+svm_pred_perf <- svm_zhao + svm_overall_pred_perf +
+  plot_layout(guides = "collect") +
+  plot_annotation(tag_levels = "a") &
+  theme(plot.tag = element_text(size = 18))
+
+svm_pred_perf
+
+ggsave(
+  here::here("figures", "final", "svm-pred-perf.pdf"),
+  svm_pred_perf,
+  width = 14,
+  height = 12,
+  units = "in"
+)