Yoshida expert-annotated marker gene analysis
Last updated: 2024-01-01
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mage_2020_marker-gene-benchmarking/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | e395540 | Jeffrey Pullin | 2023-06-18 | Add blood datasets expert analysis plots |
library(dplyr)
library(ggplot2)
library(SingleCellExperiment)
library(scater)
library(tidyr)
library(forcats)
source(here::here("code", "analysis-utils.R"))
source(here::here("code", "plot-utils.R"))
source(here::here("code", "expert-annotation-utils.R"))yoshida_results <- load_real_data_results("yoshida")
yoshida <- readRDS(here::here("data", "real_data", "yoshida.rds"))yoshida_marker_genes <- readRDS(here::here("data", "expert_mgs", "blood_expert_mgs.rds"))
intersect_clusters <- intersect(yoshida_marker_genes$cluster, unique(yoshida$label))yoshida_heatmap <- yoshida_results %>%
filter(cluster %in% intersect_clusters) %>%
plot_expert_anno_heatmap("yoshida", yoshida_marker_genes, n_top = 3,
metric = "recall") +
ggtitle("Yoshida data (3 genes selected)")
yoshida_heatmap
saveRDS(yoshida_heatmap, here::here("figures", "raw", "expert-yoshida-heatmap.rds"))yoshida_n_annotated <- yoshida_results %>%
filter(cluster %in% intersect_clusters) %>%
plot_expert_anno_n_cluster("yoshida", yoshida_marker_genes, n_top = 3) +
ggtitle("Yoshida data (3 genes selected)")
yoshida_n_annotated
saveRDS(
yoshida_n_annotated,
here::here("figures", "raw", "expert-yoshida-n-annotated.rds")
)
devtools::session_info()─ Session info ──────────────────────────────────────────────────────────────
hash: sparkle, person gesturing NO, person playing handball
setting value
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date 2024-01-01
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