update batchadjust and add copy to subset

Author: ghar1821

src/methods/batchadjust_one_control/config.vsh.yaml

@@ -67,6 +67,8 @@ resources:
   - path: /src/utils/anndata_to_fcs.R
   - path: BatchAdjust.R
   - path: utils.R
+  - type: r_script
+    path: /src/utils/helper_functions.R
 
 engines:
   # Specifications for the Docker image for this component.
@@ -77,7 +79,7 @@ engines:
     setup:
       - type: r
         bioc: [flowCore]
-        packages: [docstring]
+        packages: [docstring, dplyr]
 
 runners:
   # This platform allows running the component natively

src/methods/batchadjust_one_control/script.R

@@ -2,21 +2,23 @@ library(anndata)
 library(flowCore)
 ## VIASH START
 par <- list(
-  input = "resources_test/debug/batchadjust/_viash_par/input_1/censored_split1.h5ad",
+  input = "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/censored_split1.h5ad",
   output = "resources_test/debug/batchadjust/output.h5ad",
   percentile = as.integer('80')
 )
 meta <- list(
   name = "batchadjust_one_control",
-  temp_dir = "resources_test/tmp",
+  temp_dir = "resources_test/tmp_batchadjust_one_control",
   resources_dir = "src/methods/batchadjust_one_control"
 )
 source("src/utils/anndata_to_fcs.R")
+source("src/utils/helper_functions.R")
 ## VIASH END
 
 source(paste0(meta$resources_dir, "/utils.R"))
 source(paste0(meta$resources_dir, "/anndata_to_fcs.R"))
 source(paste0(meta$resources_dir, "/BatchAdjust.R"))
+source(paste0(meta$resources_dir, "/helper_functions.R"))
 
 tmp_dir <- get_temp_dir(meta)
 print(paste0("Using temp dir: ", tmp_dir))
@@ -39,7 +41,9 @@ on.exit(clean_temp_dir(tmp_dir))
 
 
 cat("Reading input files\n")
-input <- anndata::read_h5ad(par[["input"]])
+input <- anndata::read_h5ad(par[["input"]]) |> 
+  subset_onecontrol()
+
 #use Original_ID column to restore cell order after I/O operations
 # input$layers["preprocessed"][, "Original_ID"] <- seq(1, dim(input)[1])
 
@@ -92,8 +96,9 @@ if (!non_control_has_batch) {
 input_no_controls$obs$sample <- sapply(input_no_controls$obs$sample, fix_batch_underscore_anynum)
 
 
-cat("Writing FCS files\n")
+cat("Writing control FCS files\n")
 anndata_to_fcs(input_controls, out_dir = tmp_dir)
+cat("Writing non-control FCS files\n")
 anndata_to_fcs(input_no_controls, out_dir =  tmp_dir)
 
 cat("Writing channels to correct as a text file\n")

src/utils/helper_functions.R

@@ -86,7 +86,7 @@ subset_nocontrols <- function(adata) {
     }
 
     # Subset the adata to remove cells where is_control != 0
-    adata[adata$obs$is_control == 0, ]
+    adata[adata$obs$is_control == 0, ]$copy()
 }
 
 
@@ -112,7 +112,7 @@ subset_onecontrol <- function(adata, which_control = 1) {
     }
 
     # Subset the adata to keep cells where is_control == which_control
-    adata[adata$obs$is_control %in% c(which_control, 0), ]
+    adata[adata$obs$is_control %in% c(which_control, 0), ]$copy()
 }
 
 #' Subsets the anndata object to only include markers that need to be