Add MuSic package in the helper

openproblems-bio · Aug 27, 2024 · c191ca9 · c191ca9
1 parent bf3f65d
commit c191ca9
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Showing 3 changed files with 3 additions and 12 deletions.
diff --git a/src/helpers/utils.R b/src/helpers/utils.R
@@ -75,6 +75,8 @@ calculate_recall <- function(real_svg, sim_svg) {
 CARD_processing <- function(sp_adata, sc_adata){
   # sp_adata <- input_real_sp
   # sc_adata <- input_sc
+  library(MuSiC)
+  library(CARD)
   spatial_count <- Matrix::t(sp_adata$layers[["counts"]])
   spatial_location <- cbind.data.frame(
     x = as.numeric(sapply(strsplit(colnames(spatial_count),split="x"),"[",1)),

diff --git a/src/metrics/downstream/config.vsh.yaml b/src/metrics/downstream/config.vsh.yaml
@@ -117,8 +117,8 @@ engines:
           - dplyr
         github:
           - xzhoulab/SPARK
-          - xuranw/MuSiC
           - YingMa0107/CARD
+          - xuranw/MuSiC
 
 runners:
   - type: executable

diff --git a/src/metrics/downstream/script.R b/src/metrics/downstream/script.R
@@ -1,14 +1,3 @@
-requireNamespace("anndata", quietly = TRUE)
-requireNamespace("edgeR", quietly = TRUE)
-requireNamespace("ks", quietly = TRUE)
-requireNamespace("resample", quietly = TRUE)
-requireNamespace("reshape2", quietly = TRUE)
-requireNamespace("MuSiC", quietly = TRUE)
-requireNamespace("CARD", quietly = TRUE)
-requireNamespace("SingleCellExperiment", quietly = TRUE)
-requireNamespace("SummarizedExperiment", quietly = TRUE)
-
-
 ## VIASH START
 par <- list(
   input_spatial_dataset = "resources_test/datasets/MOBNEW/dataset_sp.h5ad",