Implement revisions

analysis/concordance.Rmd

@@ -566,7 +566,7 @@ saveRDS(
 )
 ```
 
-```{r intersection-dendrogram}
+```{r intersection-dendrogram-by-dataset}
 plot_dendrogram_by_dataset <- function(data, data_id) {
   
   n <- 10

analysis/predictive-performance.Rmd

@@ -135,7 +135,7 @@ pred_perf_data %>%
   plot_classifier_metric("median_f1_score")
 
 pred_perf_data %>% 
-  filter(data_id == "pbmc3k", classifier == "sum") %>% 
+  filter(data_id == "pbmc3k", classifier == "sum_max") %>% 
   plot_classifier_metric("median_f1_score") + 
   coord_flip(ylim = c(0.0, 1))
 

analysis/stability-simulations.Rmd

@@ -20,7 +20,7 @@ source(here::here("code", "analysis-utils.R"))
 source(here::here("code", "plot-utils.R"))
 ```
 
-```{r load-data}
+```{r}
 cluster_path <- here::here("results", "cluster_stability_sim_data")
 n_cluster_stability_data <- tibble(
   path = list.files(cluster_path, full.names = TRUE)
@@ -98,7 +98,7 @@ n_cluster_stability_plot <- n_cluster_stability_plot_data %>%
 n_cluster_stability_plot
 ```
 
-```{r load-data}
+```{r}
 path <- here::here("results", "cell_stability_sim_data")
 n_cells_stability_data <- tibble(path = list.files(path, full.names = TRUE)) %>% 
   mutate(file = basename(path)) %>%