Add negative control method that uses normally distributed data (#5)

* add a negative normal method

* fix normal method; rename folder

* make negative values positive

* rename variables

Author: rcannood

src/control_methods/negative/config.vsh.yaml

@@ -0,0 +1,22 @@
+__merge__: ../../api/comp_control_method.yaml
+
+name: negative_normal
+label: negative_normal
+summary: A negative control which generates normal distributed data.
+description: |
+  This control method generates normal distributed data as a negative control.
+  The mean and the sd are defined by the mean and sd of the input data.
+
+resources:
+  - type: r_script
+    path: script.R
+
+engines:
+  - type: docker
+    image: openproblems/base_r:1.0.0
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [midtime, midmem, midcpu]

src/control_methods/negative_normal/config.vsh.yaml

@@ -0,0 +1,39 @@
+## VIASH START
+par <- list(
+  input = "resources_test/spatialsimbench_mobnew/dataset_sp.h5ad",
+  output = "simulated_dataset.h5ad"
+)
+meta <- list(
+  name = "negative_normal"
+)
+## VIASH END
+
+cat("Reading input files\n")
+input <- anndata::read_h5ad(par$input)
+
+# generate random values
+n_rows <- nrow(input)
+n_cols <- ncol(input)
+
+values <- rnorm(n = n_rows * n_cols, mean = 3, sd = 1)
+
+# make sure all values are positive
+values[values < 0] <- abs(values[values < 0])
+
+cat("Generate outoput file\n")
+output <- anndata::AnnData(
+  layers = list(
+    counts = matrix(values, nrow = n_rows, ncol = n_cols)
+  ),
+  obs = input$obs[c("row", "col")],
+  var = input$var,
+  uns = c(
+    input$uns,
+    list(
+      method_id = meta$name
+    )
+  )
+)
+
+cat("Write output files\n")
+output$write_h5ad(par$output, compression = "gzip")

src/control_methods/negative_normal/script.R

@@ -0,0 +1,21 @@
+__merge__: ../../api/comp_control_method.yaml
+
+name: negative_shuffle
+label: negative_shuffle
+summary: A negative control method which shuffles the input data.
+description: |
+  This control method shuffles the input data as a negative control.
+
+resources:
+  - type: r_script
+    path: script.R
+
+engines:
+  - type: docker
+    image: openproblems/base_r:1.0.0
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [midtime, midmem, midcpu]

src/control_methods/negative_shuffle/config.vsh.yaml

@@ -4,7 +4,7 @@ par <- list(
   output = "simulated_dataset.h5ad"
 )
 meta <- list(
-  name = "negative"
+  name = "negative_shuffle"
 )
 ## VIASH END
 

src/control_methods/negative/script.R renamed to src/control_methods/negative_shuffle/script.R

@@ -57,7 +57,8 @@ dependencies:
   - name: methods/symsim
   - name: methods/zinbwave
   - name: control_methods/positive
-  - name: control_methods/negative
+  - name: control_methods/negative_shuffle
+  - name: control_methods/negative_normal
   - name: metrics/downstream
   - name: metrics/ks_statistic_gene_cell
   - name: metrics/ks_statistic_sc_features

src/workflows/run_benchmark/config.vsh.yaml

@@ -16,7 +16,8 @@ methods = [
   symsim,
   zinbwave,
   positive,
-  negative
+  negative_shuffle,
+  negative_normal
 ]
 
 // construct list of metrics