add cellassign predictions to repo

AlexsLemonade · Jul 14, 2023 · c505674 · c505674
1 parent 2fed6e2
commit c505674
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Showing 5 changed files with 17,973 additions and 327 deletions.
diff --git a/celltype_annotation/analysis/cellassign-combined-markers.Rmd b/celltype_annotation/analysis/cellassign-combined-markers.Rmd
@@ -57,17 +57,20 @@ panglao_comb_mtx_file <- file.path(ref_dir, "panglao_combined_mtx.csv")
 panglao_custom_mtx_file <- file.path(ref_dir, "panglao_custom_mtx.csv")
 panglao_muscle_only_mtx_file <- file.path(ref_dir, "panglao_connective_tissue_mtx.csv")
 
+# predictions output
+cellassign_outs_dir <- "cellassign_results"
+
 # cellassign predictions
 combined_prediction_file <- file.path(
-  anndata_dir, 
+  cellassign_outs_dir, 
   glue::glue("{params$library_id}_panglao_combined.tsv")
 )
 muscle_only_prediction_file <- file.path(
-  anndata_dir, 
+  cellassign_outs_dir, 
   glue::glue("{params$library_id}_panglao_connective_tissue.tsv")
 )
 custom_prediction_file <- file.path(
-  anndata_dir, 
+  cellassign_outs_dir, 
   glue::glue("{params$library_id}_panglao_custom.tsv")
 )
 

diff --git a/celltype_annotation/analysis/cellassign-combined-markers.nb.html b/celltype_annotation/analysis/cellassign-combined-markers.nb.html