Fixed rPCA

Author: LuLeom

src/methods/rpca_to_goal/config.vsh.yaml

@@ -64,6 +64,8 @@ resources:
   # The script of your component (required)
   - type: r_script
     path: script.R
+  - type: r_script
+    path: /src/utils/helper_functions.R
 
 engines:
   # Specifications for the Docker image for this component.

src/methods/rpca_to_goal/script.R

@@ -15,9 +15,12 @@ meta <- list(
 
 options(future.globals.maxSize = 25 * 1024^3)  # 25 GiB
 
+source(paste0(meta$resources_dir, "/helper_functions.R"))
+ 
 cat("Reading input files\n")
-input_adata <- anndata::read_h5ad(par[["input"]])
-
+input_adata <- anndata::read_h5ad(par[["input"]]) |>
+  subset_nocontrols()
+  
 cat("Preparing input Anndata\n")
 input_adata$obs$batch <- as.factor(input_adata$obs$batch)
 

src/methods/rpca_to_mid/config.vsh.yaml

@@ -68,7 +68,8 @@ resources:
   # The script of your component (required)
   - type: r_script
     path: script.R
-
+  - type: r_script
+    path: /src/utils/helper_functions.R
 engines:
   # Specifications for the Docker image for this component.
   - type: docker

src/methods/rpca_to_mid/script.R

@@ -15,9 +15,11 @@ meta <- list(
 
 options(future.globals.maxSize = 25 * 1024^3)  # 25 GiB
 
-
+source(paste0(meta$resources_dir, "/helper_functions.R"))
+ 
 cat("Reading input files\n")
-input_adata <- anndata::read_h5ad(par[["input"]])
+input_adata <- anndata::read_h5ad(par[["input"]]) |>
+  subset_nocontrols()
 
 cat("Preparing input Anndata\n")
 input_adata$obs$batch <- as.factor(input_adata$obs$batch)