new fig3

pipeline/figures/figure3.R

@@ -44,63 +44,3 @@ pdf("output/v8/paper-figures/figure3-overall-benchmark.pdf", height = 8.4, width
   eval
 dev.off()
 
-space_eval <- (plot_spacer() | eval) + 
-  plot_layout(widths = c(0.001, 1))
-
-pdf("output/v8/paper-figures/figure3.pdf", height = 12, width = 9)
-  schematic / wrap_elements(full = space_eval) + 
-    plot_annotation(tag_levels = "A") + 
-    plot_layout(heights = c(1.7, 4))
-dev.off()
-
-
-
-
-sel_acc <- filter(acc, corrupted == 0) |> 
-  filter(AL_alg == "rf" | is.na(AL_alg)) |> 
-  filter(rand == 0 | is.na(rand)) |> 
-  filter(.metric == "f_meas") |> 
-  filter(initial == "ranking" | is.na(initial))
-
-
-cross_cohort_ranks <- get_ranked_mean_estimate_by_cohort(sel_acc)
-method_order <- get_cross_cohort_mean_ranked_estimate(cross_cohort_ranks) |> 
-  pull(selection_procedure)
-
-sel_acc |> 
-  group_by(selection_procedure, cell_num, cohort) |> 
-  mutate(selection_procedure = factor(selection_procedure, levels = method_order),
-         mean_estimate = mean(.estimate),
-         lower_quant = quantile(na.omit(.estimate), 0.25),
-         upper_quant = quantile(na.omit(.estimate), 0.75)) |> 
-  ggplot() +
-  aes(fill = selection_procedure) +
-  geom_segment(aes(x = as.character(cell_num),
-                   y = lower_quant, yend = upper_quant),
-               position = position_dodge(width = 0.9)) +
-  geom_point(aes(x = as.character(cell_num), y = mean_estimate, colour = selection_procedure),
-             position = position_dodge(width = 0.9)) +
-  scale_color_manual(values = sel_meth_cols) +
-  whatsthatcell_theme() +
-  facet_wrap(~cohort, scales = "free_y", nrow = 1) +
-  labs(title = metric) +
-  theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))
-
-
-devtools::load_all("../ggplot2/")
-p <- sel_acc |> 
-  filter(cohort == "scRNASeq" & cell_num == 100) |> 
-  group_by(selection_procedure, cell_num, cohort) |> 
-  mutate(selection_procedure = factor(selection_procedure, levels = method_order),
-         mean_estimate = mean(.estimate),
-         lower_quant = quantile(na.omit(.estimate), 0.25),
-         upper_quant = quantile(na.omit(.estimate), 0.75)) |> 
-  ggplot(aes(cell_num, mean_estimate, colour = selection_procedure))
-
-# Want the ends stay stable? Define them.
-p + geom_segment(
-  aes(xend = cell_num, yend = 0),
-  position = position_dodge(width = 0.9)
-)
-
-p + geom_segment(aes(yend = 0), position = position_dodge(width = 0.8))