From 263219374f45b50a60257068fbeec2fc0b3d2282 Mon Sep 17 00:00:00 2001
From: Jeffrey Pullin <jpullin@svi.edu.au>
Date: Mon, 1 Jan 2024 00:34:34 +1100
Subject: [PATCH] Implement revisions
---
analysis/concordance.Rmd | 2 +-
analysis/predictive-performance.Rmd | 2 +-
analysis/stability-simulations.Rmd | 4 ++--
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/analysis/concordance.Rmd b/analysis/concordance.Rmd
index e4f1066..9957550 100644
--- a/analysis/concordance.Rmd
+++ b/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
diff --git a/analysis/predictive-performance.Rmd b/analysis/predictive-performance.Rmd
index 56004d2..30a9ac0 100644
--- a/analysis/predictive-performance.Rmd
+++ b/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))
diff --git a/analysis/stability-simulations.Rmd b/analysis/stability-simulations.Rmd
index dc08c87..0cd7d93 100644
--- a/analysis/stability-simulations.Rmd
+++ b/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)) %>%
--
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