Zeisel expert-annotated marker gene analysis
Last updated: 2024-01-01
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Knit directory:
mage_2020_marker-gene-benchmarking/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | fcecf65 | Jeffrey Pullin | 2022-09-09 | Build site. |
| html | af96b34 | Jeffrey Pullin | 2022-08-30 | Build site. |
| Rmd | 9dccf15 | Jeffrey Pullin | 2022-08-30 | Update all analyses |
| html | 4ced4aa | Jeffrey Pullin | 2022-05-20 | Build site. |
| Rmd | f61c73a | Jeffrey Pullin | 2022-05-20 | Add number of cluster annotated analysis |
| html | f61c73a | Jeffrey Pullin | 2022-05-20 | Add number of cluster annotated analysis |
| html | 0e47874 | Jeffrey Pullin | 2022-05-04 | Build site. |
| html | 048156f | Jeffrey Pullin | 2022-05-02 | Tweak analysis outputs |
| html | 8b989e1 | Jeffrey Pullin | 2022-05-02 | Build site. |
| Rmd | 2e627e5 | Jeffrey Pullin | 2022-05-02 | Refresh all analyses |
library(dplyr)
library(ggplot2)
library(SingleCellExperiment)
library(scater)
library(tidyr)
library(forcats)
library(patchwork)
source(here::here("code", "analysis-utils.R"))
source(here::here("code", "plot-utils.R"))
source(here::here("code", "expert-annotation-utils.R"))zeisel_results <- load_real_data_results("zeisel")
zeisel <- readRDS(here::here("data", "special_real_data", "zeisel.rds"))zeisel_marker_genes <- tribble(
~cluster, ~expert_mgs,
"interneurons", "Pnoc",
"pyramidal SS", "Tbr1",
"pyramidal CA1", "Spink8",
"oligodendrocytes", "Hapln2",
"microglia", "Aif1",
"endothelial-mural", "Acta2",
"astrocytes_ependymal", "Aldoc"
) 10 genes
plot_expert_anno_heatmap(
zeisel_results,
"zeisel",
zeisel_marker_genes,
metric = "recall",
n_top = 10
)
20 genes
expert_zeisel_heatmap <- plot_expert_anno_heatmap(
zeisel_results,
"zeisel",
zeisel_marker_genes,
metric = "recall",
n_top = 20
) +
ggtitle("Zeisel data (At most 20 genes selected)")
expert_zeisel_heatmap
saveRDS(
expert_zeisel_heatmap,
here::here("figures", "raw", "expert-zeisel-heatmap.rds")
)expert_zeisel_n_annotated <- plot_expert_anno_n_cluster(
zeisel_results,
"zeisel",
zeisel_marker_genes,
n_top = 20
) +
ggtitle("Zeisel data (At most 20 genes selected)")
expert_zeisel_n_annotated
saveRDS(
expert_zeisel_n_annotated,
here::here("figures", "raw", "expert-zeisel-n-annotated.rds")
)Expert marker genes
plotExpression(zeisel, x = "label", zeisel_marker_genes$expert_mgs) +
theme(axis.text.x = element_text(angle = 30, hjust = 1))
Selected oligodendrocytes markers
Mog is a known marker
seurat_wilcox <- readRDS(
here::here("results", "real_data", "zeisel-seurat_wilcox.rds")
)
top_mgs <- seurat_wilcox$result %>%
filter(cluster == "oligodendrocytes") %>%
head(n = 10) %>%
pull(gene)
seurat_wilcox_top_oligodedrocyte <- plotExpression(zeisel, x = "label", top_mgs) +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
seurat_wilcox_top_oligodedrocyte
ggsave(
here::here("figures", "final", "seurat-wilcox-top-oligodencrocytes.pdf"),
seurat_wilcox_top_oligodedrocyte,
width = 8,
height = 8,
units = "in"
)Selected interneurons - Seurat t-test
seurat_t <- readRDS(
here::here("results", "real_data", "zeisel-seurat_t.rds")
)
seurat_t$result %>%
filter(cluster == "interneurons") %>%
print(n = 2)# A tibble: 1,369 × 7
p_value p_value_adj cluster log_fc gene raw_statistic scaled_statistic
<dbl> <dbl> <fct> <dbl> <chr> <dbl> <dbl>
1 1.05e-221 2.11e-218 interneurons 0.977 Snap… 0 0
2 5.21e-216 1.04e-212 interneurons 1.84 Ndrg4 0 0
# … with 1,367 more rowsinterneuron_seurat_t <- plotExpression(zeisel, x = "label", c("Snap25", "Ndrg4")) +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
interneuron_seurat_t
Selected interneurons - Scran t-test any
scran_t_any <- readRDS(
here::here("results", "real_data", "zeisel-scran_findMarkers_t_any.rds")
)
scran_t_any$result %>%
filter(cluster == "interneurons") %>%
print(n = 2)# A tibble: 2,003 × 8
p_value raw_statistic p_value_adj gene top scaled_statistic cluster
<dbl> <dbl> <dbl> <chr> <int> <dbl> <chr>
1 0 -4.96 0 Mag 1 0 interneuro…
2 7.28e-270 -3.13 3.10e-268 Neurod6 1 0 interneuro…
# … with 2,001 more rows, and 1 more variable: log_fc <dbl>interneuron_scran_t_any <- plotExpression(zeisel, x = "label", c("Mag", "Neurod6")) +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
interneuron_scran_t_any
seurat_t_scran_any_t <- interneuron_seurat_t / interneuron_scran_t_any +
plot_annotation(tag_levels = "a") &
theme(plot.tag = element_text(size = 18))
seurat_t_scran_any_t
ggsave(
here::here("figures", "final", "seurat-t-scran-any-t.pdf"),
seurat_t_scran_any_t,
width = 8,
height = 8,
units = "in"
)
devtools::session_info()─ Session info ──────────────────────────────────────────────────────────────
hash: hospital, woman cook: medium skin tone, water pistol
setting value
version R version 4.1.2 (2021-11-01)
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date 2024-01-01
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