Add script to create manuscript figures

code/manuscript-figures.R

+library(ggplot2)
+library(patchwork)
+
+# Conceptual figure (components)
+
+rank_rank <- readRDS(
+  here::here("figures", "raw", "rank-rank-scanpy-default-seurat-default.rds")
+)
+
+prop_intersect <- readRDS(
+  here::here("figures", "raw", "scanpy-seurat-intersection.rds")
+)
+
+conceptual_figure_bottom <- prop_intersect + rank_rank +
+  plot_layout(nrow = 1, widths = c(1, 1))
+
+conceptual_figure_bottom
+
+ggsave(
+  filename = here::here("figures", "final", "conceptual-figure-bottom.pdf"),
+  plot = conceptual_figure_bottom,
+  width = 12, height = 4, units = "in"
+)
+
+raw_tsne <- readRDS(
+  here::here("figures", "raw", "raw-tsne.rds")
+)
+
+ggsave(
+  filename = here::here("figures", "final", "raw-tsne.pdf"),
+  plot = raw_tsne,
+  width = 4, height = 4, units = "in"
+)
+
+coloured_tsne <- readRDS(
+  here::here("figures", "raw", "raw-tsne.rds")
+)
+
+ggsave(
+  filename = here::here("figures", "final", "coloured-tsne.pdf"),
+  plot = coloured_tsne,
+  width = 4, height = 4, units = "in"
+)
+
+ms4a1_expression <- readRDS(
+  here::here("figures", "raw", "ms4a1-expression.rds")
+)
+
+ggsave(
+  filename = here::here("figures", "final", "ms4a1-expression.pdf"),
+  plot = ms4a1_expression,
+  width = 4, height = 4, units = "in"
+)
+
+# Method concordance + characteristics figure
+
+concordance_dendorogram <- readRDS(
+  here::here("figures", "raw", "dendrogram.rds")
+)
+
+raw_info <- readRDS(
+  here::here("figures", "raw", "raw-info.rds")
+) +
+  theme(plot.margin = margin(-1, -1, 1, -1, "cm"))
+
+strategy_info <- readRDS(
+  here::here("figures", "raw", "strategy-info.rds")
+) +
+  theme(plot.margin = margin(-1, -1, -1, -1, "cm"))
+
+package_info <- readRDS(
+  here::here("figures", "raw", "package-info.rds")
+) +
+  theme(plot.margin = margin(-1, -1, -1, -1, "cm"))
+
+overall_prop_up <- readRDS(
+  here::here("figures", "raw", "overall-prop-up.rds")
+) +
+  ggtitle("Regulation direction across datasets")
+
+all_n_zero_pvalues <- readRDS(
+  here::here("figures", "raw", "all_n_zero_pvalues.rds")
+) +
+  ggtitle("Number of zero p-values across datasets")
+
+full_dendrogram <- concordance_dendorogram +
+  package_info +
+  raw_info +
+  strategy_info +
+  plot_layout(
+    nrow = 1,
+    widths = c(0.9, 0.02, 0.02, 0.02),
+    heights = c(4, 1, 1, 1),
+    guides = "collect"
+  )
+
+full_dendrogram
+
+concordance_figure <- full_dendrogram / (overall_prop_up + all_n_zero_pvalues) +
+  plot_layout(heights = c(3, 2), tag_level = "new") +
+  plot_annotation(tag_levels = list(c("a", " ", " ", " ", "b", "c")))
+
+concordance_figure
+
+ggsave(
+  filename = here::here("figures", "final", "concordance-figure.pdf"),
+  plot = concordance_figure,
+  width = 16,
+  height = 16,
+  units = "in"
+)
+
+# Computational performance + implementation quality figure
+
+overall_time <- readRDS(here::here("figures", "raw", "overall-time.rds"))
+overall_memory <- readRDS(here::here("figures", "raw", "overall-memory.rds"))
+num_cells_time <- readRDS(here::here("figures", "raw", "time-num-cells.rds")) +
+  theme(axis.title.y = element_text(margin = margin(r = -120, unit = "pt")))
+implementation_quality <- readRDS(here::here("figures", "raw", "implementation.rds"))
+
+# Warning is spurious
+top <- overall_time + overall_memory
+bottom <- num_cells_time + implementation_quality +
+  plot_layout(widths = c(2, 1))
+
+computational_performance_figure <- top / bottom +
+  plot_annotation(tag_levels = "a")
+
+computational_performance_figure
+
+ggsave(
+  filename = here::here("figures", "final", "computational-performance-figure.pdf"),
+  plot = computational_performance_figure,
+  width = 16,
+  height = 16,
+  units = "in"
+)
+
+# Simulated performance figure
+
+overall_recall <- readRDS(
+  here::here("figures", "raw", "overall-recall.rds")
+) +
+  ggtitle("Recall")
+
+overall_precision <- readRDS(
+  here::here("figures", "raw", "overall-precision.rds")
+) +
+  ggtitle("Precision") +
+  theme(axis.title.y = element_blank())
+
+overall_f1_score <- readRDS(
+  here::here("figures", "raw", "overall-f1-score.rds")
+) +
+  ggtitle("F1 score") +
+  theme(axis.title.y = element_blank())
+
+simulated_perf_figure <- overall_recall + overall_precision + overall_f1_score +
+  plot_layout(guides = "collect") +
+  plot_annotation(tag_levels = "a")
+
+simulated_perf_figure
+
+ggsave(
+  filename = here::here("figures", "final", "simulated-perf-figure.pdf"),
+  plot = simulated_perf_figure,
+  width = 12,
+  height = 8,
+  units = "in"
+)
+
+# Expert performance figure
+
+expert_lawlor_heatmap <- readRDS(
+  here::here("figures", "raw", "expert-lawlor-heatmap.rds")
+)
+
+expert_pbmc3k_heatmap <- readRDS(
+  here::here("figures", "raw", "expert-pbmc3k-heatmap.rds")
+)
+
+expert_perf_figure <- expert_lawlor_heatmap + expert_pbmc3k_heatmap +
+  plot_layout(ncol = 2) +
+  plot_annotation(tag_levels = "a")
+
+expert_perf_figure
+
+ggsave(
+  filename = here::here("figures", "final", "expert-perf-figure.pdf"),
+  plot = expert_perf_figure,
+  width = 16,
+  height = 10,
+  units = "in"
+)
+
+# Predictive performance figure
+
+zhao_pred_perf <- readRDS(
+  here::here("figures", "raw", "zhao-pred-perf.rds")
+)
+
+overall_multiclass_pred_plot <- readRDS(
+  here::here("figures", "raw", "overall-mc-pred-plot.rds")
+)
+
+pbmc3k_seurat_wilcox_confmat <- readRDS(
+  here::here("figures", "raw", "pbmc3k-seurat-wilcox-confmat.rds")
+)
+
+lhs <- (zhao_pred_perf / pbmc3k_seurat_wilcox_confmat) +
+  plot_layout(ncol = 1, heights = c(2, 1))
+pred_perf_figure <- lhs - overall_multiclass_pred_plot +
+  plot_layout(ncol = 2) +
+  plot_annotation(tag_levels = "a")
+
+pred_perf_figure
+
+ggsave(
+  filename = here::here("figures", "final", "pred-perf-figure.pdf"),
+  plot = pred_perf_figure,
+  width = 14,
+  height = 14,
+  units = "in"
+)
+
+# Case studies figure
+
+log_fc_plot <- readRDS(
+  here::here("figures", "raw", "log-fc-b-cluster-scatter.rds")
+)
+welch_issue_plot <- readRDS(
+  here::here("figures", "raw", "rr-scanpy-t-abs-seurat-t.rds")
+)
+logfc_abs_prop_intersect_plot <- readRDS(
+  here::here("figures", "raw", "logfc-abs-prop-intersect.rds")
+)
+scanpy_seurat_zeisel_oligodendrocytes_plot <- readRDS(
+  here::here("figures", "raw", "scanpy-seurat-zeisel-oligodendrocytes.rds")
+)
+
+case_studies_figure <- logfc_abs_prop_intersect_plot +
+  scanpy_seurat_zeisel_oligodendrocytes_plot +
+  log_fc_plot +
+  welch_issue_plot +
+  plot_layout(ncol = 2) +
+  plot_annotation(tag_levels = "a") &
+  theme(plot.tag = element_text(size = 18))
+
+case_studies_figure
+
+ggsave(
+  filename = here::here("figures", "final", "case-studies-figure.pdf"),
+  plot = case_studies_figure,
+  width = 16,
+  height = 16,
+  units = "in"
+)
+
+# Supplementary figures
+
+# Additional expert heatmaps
+
+expert_ss3_pbmc3_heatmap <- readRDS(
+  here::here("figures", "raw", "expert-ss3_pbmc-heatmap.rds")
+) +
+  theme(legend.position = "none")
+expert_zeisel_heatmap <- readRDS(
+  here::here("figures", "raw", "expert-zeisel-heatmap.rds")
+)
+
+ss3_pbmc_zeisel_expert_heatmaps <- expert_ss3_pbmc3_heatmap + expert_zeisel_heatmap  +
+  plot_annotation(tag_levels = "a")
+
+ggsave(
+  here::here("figures", "final", "ss3_pbmc-zeisel-expert-heatmaps.pdf"),
+  ss3_pbmc_zeisel_expert_heatmaps,
+  width = 8,
+  height = 8,
+  units = "in"
+)
+
+# Number of clusters simulations
+
+time_num_clusters <- readRDS(here::here("figures", "raw", "time-num-clusters.rds"))
+memory_num_clusters <- readRDS(here::here("figures", "raw", "memory-num-clusters.rds"))
+
+num_cluster_sims <- time_num_clusters + memory_num_clusters +
+  plot_annotation(tag_levels = "a")
+
+ggsave(
+  here::here("figures", "final", "num-clusters-sims.pdf"),
+  num_cluster_sims,
+  width = 20,
+  height = 12,
+  units = "in"
+)
+
+# Zero expression consequences
+
+all_logfc_scatter <- readRDS(
+  here::here("figures", "raw", "log-fc-scatter.rds")
+) +
+  ggtitle("pbmc3k data")
+volcano_plot <- readRDS(
+  here::here("figures", "raw", "volcano-plot.rds")
+)
+zero_expression <- all_logfc_scatter + volcano_plot +
+  plot_annotation(tag_levels = "a")
+zero_expression
+
+ggsave(
+  here::here("figures", "final", "zero-expression.pdf"),
+  zero_expression,
+  width = 12,
+  height = 8,
+  units = "in"
+)
+