consensus calculation using HPCell function

Author: stemangiola

dev/HCA_cell_type_consensus.R

@@ -0,0 +1,55 @@
+library(arrow)
+library(dplyr)
+library(duckdb)
+library(HPCell)
+
+# Read the Parquet file into an R data frame
+con <- dbConnect(duckdb::duckdb(), dbdir = ":memory:")
+parquet_file = "/vast/projects/cellxgene_curated/census_samples/concensus_input.parquet"
+
+data_tbl <- tbl(con, sql(paste0("SELECT * FROM read_parquet('", parquet_file, "')")))
+
+annotation_combination = 
+  data_tbl |> 
+  #select(azimuth_predicted.celltype.l2, monaco_first.labels.fine, blueprint_first.labels.fine) |> 
+  select(cell_, dataset_id, cell_type, cell_type_ontology_term_id, azimuth_predicted.celltype.l2, monaco_first.labels.fine, blueprint_first.labels.fine)  
+  #arrange(desc(n)) |> 
+
+
+
+
+
+annotation_consensus  = 
+  annotation_combination |>
+  distinct(azimuth_predicted.celltype.l2, monaco_first.labels.fine, blueprint_first.labels.fine) |> 
+  as_tibble() |> 
+  mutate(reannotation_consensus = reference_annotation_to_consensus(azimuth_input = azimuth_predicted.celltype.l2, monaco_input = monaco_first.labels.fine, blueprint_input = blueprint_first.labels.fine )) 
+
+
+annotation_combination = 
+  annotation_combination |> 
+  left_join(annotation_consensus, copy = TRUE)
+
+output_parquet <- "/vast/projects/mangiola_immune_map/PostDoc/CuratedAtlasQueryR/dev/consensus_output.parquet"
+
+# Use DuckDB's COPY TO command to write the data back to Parquet
+# We need to execute a SQL command using dbExecute()
+copy_query <- paste0("
+  COPY (
+    SELECT *
+    FROM (
+      ", dbplyr::sql_render(annotation_combination), "
+    )
+  ) TO '", output_parquet, "' (FORMAT PARQUET);
+")
+
+# Execute the COPY command
+dbExecute(con, copy_query)
+
+# Disconnect from the database
+dbDisconnect(con, shutdown = TRUE)
+
+# Read back
+con <- dbConnect(duckdb::duckdb(), dbdir = ":memory:")
+data_consensus <- tbl(con, sql(paste0("SELECT * FROM read_parquet('", output_parquet, "')")))
+