disable execution cache, subset before pseudobulk

_quarto.yml

@@ -29,4 +29,3 @@ format:
 # cache computations
 execute:
   freeze: auto
-  cache: true

notebooks/usecase.qmd

@@ -55,8 +55,21 @@ adata <- read_h5ad("usecase_data/sc_counts_reannotated_with_counts.h5ad")
 adata
 ```
 
+## 3. Subset data
 
-## 3. Compute pseudobulk
+Subset to a single small molecule and control for computational efficiency:
+
+```{python select_sm_celltype}
+sm_name = "Belinostat"
+control_name = "Dimethyl Sulfoxide"
+
+adata = adata[
+  adata.obs["sm_name"].isin([sm_name, control_name])
+]
+```
+
+
+## 4. Compute pseudobulk
 
 ```{python import_pandas}
 import pandas as pd
@@ -97,7 +110,7 @@ Store to disk:
 pb_adata.write_h5ad("usecase_data/pseudobulk.h5ad")
 ```
 
-## 4. Compute DE
+## 5. Compute DE
 
 ```{r load_pbdata}
 library(anndata)
@@ -118,13 +131,10 @@ Create DESeq dataset:
 count_data <- t(pb_adata$X)
 storage.mode(count_data) <- "integer"
 
-# subset to small molecule and control
-ix <- pb_adata$obs$sm_name %in% c(sm_name, control_name)
-
 # create dataset
 dds <- DESeq2::DESeqDataSetFromMatrix(
-  countData = count_data[, ix],
-  colData = pb_adata$obs[ix, ],
+  countData = count_data,
+  colData = pb_adata$obs,
   design = ~ sm_name + cell_type + plate_name,
 )
 ```