Update astrocyte analysis

analysis/astrocyte-case-study.Rmd

@@ -10,6 +10,9 @@ knitr::opts_chunk$set(echo = TRUE)
 ```{r libraries}
 library(SingleCellExperiment)
 library(dplyr)
+library(purrr)
+library(tibble)
+library(scater)
 ```
 
 ```{r load-data}
@@ -21,15 +24,76 @@ scanpy_default <- readRDS(
   here::here("results", "real_data", "astrocyte-scanpy_t_rankby_raw.rds")
 )
 
-# FIXME: The sorting should not be needed...
-scanpy_default$result %>% 
-  filter(cluster == "Astro_THAL_hab") %>% 
-  arrange(desc(scaled_statistic))
-
 seurat_default <- readRDS(
   here::here("results", "real_data", "astrocyte-seurat_wilcox.rds")
 )
+```
+
+Work on Astro_THAL_Lat for now.
+
+```{r}
+scanpy_default |> 
+  pluck("result") |> 
+  as_tibble() |> 
+  filter(cluster == "Astro_THAL_lat")
+
+seurat_default |> 
+  pluck("result") |> 
+  as_tibble() |> 
+  filter(cluster == "Astro_THAL_lat")
+```
+
+Only Seurat finds Car10
 
-seurat_default$result %>% 
-  filter(cluster == "Astro_THAL_hab")
+```{r}
+scanpy_default |> 
+  pluck("result") |> 
+  as_tibble() |> 
+  filter(cluster == "Astro_THAL_lat") |> 
+  mutate(n = 1:n()) |> 
+  filter(gene == "Car10")
 ```
+
+Astro_STR
+
+Efemp1, Gfra1, Thbs4, Zfhx3
+
+```{r}
+scanpy_default |> 
+  pluck("result") |> 
+  as_tibble() |> 
+  filter(cluster == "Astro_STR")
+
+seurat_default |> 
+  pluck("result") |> 
+  as_tibble() |> 
+  filter(cluster == "Astro_STR")
+
+plotExpression(astrocyte, x = "label", "Efemp1")
+plotExpression(astrocyte, x = "label", "Cst3")
+plotExpression(astrocyte, x = "label", "Kcnd2")
+plotExpression(astrocyte, x = "label", "Gfra1")
+plotExpression(astrocyte, x = "label", "Slc1a2")
+plotExpression(astrocyte, x = "label", "Lrp1b")
+plotExpression(astrocyte, x = "label", "Erbb4")
+```
+
+Kcnd2 down-regulated
+
+```{r}
+scanpy_default |> 
+  pluck("result") |> 
+  as_tibble() |> 
+  filter(cluster == "Astro_HPC")
+
+seurat_default |> 
+  pluck("result") |> 
+  as_tibble() |> 
+  filter(cluster == "Astro_HPC")
+
+plotExpression(astrocyte, x = "label", "Slc1a2")
+plotExpression(astrocyte, x = "label", "Pdgfd")
+plotExpression(astrocyte, x = "label", "Cadps")
+plotExpression(astrocyte, x = "label", "Kcnd2")
+```
+