add recall curve

r/1_npdr_cc.Rmd

@@ -275,15 +275,28 @@ auroc_npdr_cc <- ss_npdr$auc
 auroc_relief_cc <- ss_relief$auc
 auroc_rf_cc <- ss_rf$auc
 
-ss_df_cc <- data.frame(Sensitivity = c(ss_npdr$sensitivities, 
-                                       ss_relief$sensitivities,
-                                       ss_rf$sensitivities), 
-                    Specificity = c(ss_npdr$specificities, 
-                                    ss_relief$specificities,
-                                    ss_rf$specificities)) %>%
-  mutate(type = c(rep('NPDR', length(ss_npdr$sensitivities)),
-                  rep('Relief', length(ss_relief$sensitivities)),
-                  rep('Random forest', length(ss_rf$sensitivities))))
+ss_df_cc <- data.frame(
+  Sensitivity = c(
+    ss_npdr$sensitivities,
+    ss_relief$sensitivities,
+    ss_rf$sensitivities
+  ),
+  Specificity = c(
+    ss_npdr$specificities,
+    ss_relief$specificities,
+    ss_rf$specificities
+  )
+) %>%
+  mutate(type = c(
+    rep('NPDR', length(ss_npdr$sensitivities)),
+    rep('Relief', length(ss_relief$sensitivities)),
+    rep('Random forest', length(ss_rf$sensitivities))
+  ),
+  pct_selected = c(
+    seq(1, 0, length.out = length(ss_npdr$sensitivities)),
+    seq(1, 0, length.out = length(ss_relief$sensitivities)),
+    seq(1, 0, length.out = length(ss_rf$sensitivities))
+  ))
 ```
 
 

r/1_npdr_qtrait.Rmd

@@ -224,14 +224,28 @@ auroc_npdr_qtrait <- ss_npdr$auc
 auroc_relief_qtrait <- ss_relief$auc
 auroc_rf_qtrait <- ss_rf$auc
 
-ss_df_qtrait <- data.frame(Sensitivity = c(ss_npdr$sensitivities, 
-                                       ss_relief$sensitivities,
-                                       ss_rf$sensitivities), 
-                    Specificity = c(ss_npdr$specificities, ss_relief$specificities,
-                                    ss_rf$specificities)) %>%
-  mutate(type = c(rep('NPDR', length(ss_npdr$sensitivities)),
-                  rep('Relief', length(ss_relief$sensitivities)),
-                  rep('Random forest', length(ss_rf$sensitivities))))
+ss_df_qtrait <- data.frame(
+  Sensitivity = c(
+    ss_npdr$sensitivities,
+    ss_relief$sensitivities,
+    ss_rf$sensitivities
+  ),
+  Specificity = c(
+    ss_npdr$specificities,
+    ss_relief$specificities,
+    ss_rf$specificities
+  )
+) %>%
+  mutate(type = c(
+    rep('NPDR', length(ss_npdr$sensitivities)),
+    rep('Relief', length(ss_relief$sensitivities)),
+    rep('Random forest', length(ss_rf$sensitivities))
+  ),
+  pct_selected = c(
+    seq(1, 0, length.out = length(ss_npdr$sensitivities)),
+    seq(1, 0, length.out = length(ss_relief$sensitivities)),
+    seq(1, 0, length.out = length(ss_rf$sensitivities))
+  ))
 ```
 
 

r/3_visualize_simulation.Rmd

@@ -6,7 +6,7 @@ output: html_document
 Combine plots together:
 
 ```{r}
-rm(list = ls())
+# rm(list = ls())
 load('results/df_cc.Rdata')
 load('results/df_qtrait.Rdata')
 load('results/rf_cc.Rdata')
@@ -305,6 +305,29 @@ roc
 ```
 
 
+```{r}
+recall_text <- data.frame(
+  label = c('Random forest','Random forest',
+            'RRelief', 'Relief-F',
+            'NPDR', 'NPDR'),
+  sim = rep(c('Continuous outcome', 'Dichotomous outcome'), 3),
+  x = c(0.47, 0.65, 0.16, 0.17, 0.28, 0.3), 
+  y = c(0.5, 0.6, 0.15, 0.15, 0.85, 0.85), 
+  type = rep(c('Random forest', 'Relief', 'NPDR'), each = 2)
+)
+
+recall <- ggplot(ss_df, aes(x = pct_selected, y = Sensitivity, color = type)) +   
+  geom_path(size = 0.8) + theme_bw() + facet_wrap(~ sim) + coord_fixed(ratio = 1) +
+  scale_color_manual(values = cbbPalette[c(8,3,6)]) + guides(color = FALSE) +
+  scale_x_continuous(breaks = seq(1, 0, -0.2), labels = scales::percent) + 
+  scale_y_continuous(breaks = seq(0, 1, 0.2), labels = scales::percent) + 
+  labs(x = 'Selection percentage cutoff', y = 'Recall') +
+  geom_text(recall_text, mapping = aes(x = x, y = y, label = label), size = 3)
+
+recall
+ggsave(recall, filename = paste0('figs/recall_compare_1.pdf'), height = 3, width = 5)
+```
+
 # Replications of auROC for Supplement:
 
 Must run `2_npdr_relief_100_cc_auroc.Rmd` and `2_npdr_relief_100_qtrait_auroc.Rmd`: