Adjust initial cell2location data analysis

analysis/cell2location-astrocyte-exploration.Rmd

@@ -10,16 +10,26 @@ knitr::opts_chunk$set(echo = TRUE)
 ```{r libraries}
 library(zellkonverter)
 library(SingleCellExperiment)
-library(SeuratDisk)
 ```
 
 ```{r load-data}
-path <- here::here(
+all_cells_path <- here::here(
+  "data", 
+  "all_cells_20200625.h5ad"
+)
+
+all_cells_data <- readH5AD(all_cells_path)
+
+all_cells_data$total_counts
+
+
+astro_path <- here::here(
   "data", 
   "downloaded_data",
   "mouse_brain_snRNA_with_UMAP_astrocytes_cellxgene.h5ad"
 )
-astro_data <- readH5AD(path)
+
+astro_data <- readH5AD(astro_path)
 
 astro_data
 
@@ -42,6 +52,6 @@ plotUMAP(astro_data, colour_by = "annotation_1")
 anno <- as.character(colData(astro_data)[["annotation_1"]])
 # Remove the "Astro_" prefix. 
 anno <- substr(anno, 7, nchar(anno))
+```
 
 
-```