git pull

Merge branch 'master' of github.com:stemangiola/HCAquery

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# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

Author: stemangiola

DESCRIPTION

@@ -11,6 +11,8 @@ Depends:
     R (>= 4.1.0)
 Imports:
 	dplyr,
+	SummarizedExperiment,
+	SingleCellExperiment,
 	tidySingleCellExperiment,
 	purrr,
 	zellkonverter,

NAMESPACE

@@ -8,6 +8,8 @@ importFrom(HDF5Array,HDF5RealizationSink)
 importFrom(HDF5Array,loadHDF5SummarizedExperiment)
 importFrom(RSQLite,SQLITE_RO)
 importFrom(RSQLite,SQLite)
+importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SummarizedExperiment,colData)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,pull)
 importFrom(dplyr,tbl)

R/query.R

@@ -15,6 +15,8 @@
 #' @importFrom stringr str_remove
 #' @importFrom HDF5Array HDF5RealizationSink
 #' @importFrom HDF5Array loadHDF5SummarizedExperiment
+#' @importFrom SingleCellExperiment SingleCellExperiment
+#' @importFrom SummarizedExperiment colData
 #'
 #' @export
 #'
@@ -53,24 +55,9 @@ get_SingleCellExperiment = function(.data, repository = "/vast/projects/RCP/huma
 		unlist() |>
 		unique()
 
-	sce =
-		sce |>
-		map(~ {
-			missing_genes = all_genes  |> setdiff(rownames(.x))
-
-			missing_matrix =
-				HDF5RealizationSink(c(length(missing_genes),ncol(.x)), as.sparse = TRUE) |>
-				as("DelayedArray")
-
-			rownames(missing_matrix) = missing_genes
-			colnames(missing_matrix) = colnames(.x)
-
-			missing_sce = SingleCellExperiment(list(X=missing_matrix),  colData=colData(.x))
-			missing_sce@int_colData = .x@int_colData
-
-			# Make cell name unique
-			.x |> rbind(missing_sce	)
-		})
+	# Drop files with one cell, which causes
+	# the DFrame objects to combine must have the same column names
+	sce = sce[map_int(sce, ncol)>1]
 
 	cat("\n")
 

dev/DB2_files.R

@@ -17,14 +17,16 @@ library(HCAquery)
 options(scipen = 999)
 #
 
-# # CREATE MAKEFILE
-# tab = "\t"
-# root_directory = "/vast/projects/RCP/human_cell_atlas"
-# raw_data_directory = glue("{root_directory}/raw_data")
-# splitted_DB2_data_directory = glue("{root_directory}/splitted_DB2_data")
-# file_cell_types_directory = glue("{root_directory}/file_cell_types")
-# input_files_path = dir(file_cell_types_directory, full.names = TRUE)
-# #
+# CREATE MAKEFILE
+tab = "\t"
+root_directory = "/vast/projects/RCP/human_cell_atlas"
+raw_data_directory = glue("{root_directory}/raw_data")
+splitted_DB2_data_directory = glue("{root_directory}/splitted_DB2_data")
+file_cell_types_directory = glue("{root_directory}/file_cell_types")
+input_files_path = dir(file_cell_types_directory, full.names = TRUE)
+gene_names = glue("{root_directory}/gene_names.rds")
+#
+#
 # ## metadata = readRDS(metadata_path)
 #
 # get_metadata() |>
@@ -67,7 +69,7 @@ options(scipen = 999)
 # 			c(
 # 				glue("CATEGORY=split_data{..4}\nMEMORY={..3}\nCORES=1\nWALL_TIME=30000"),
 # 				glue(
-# 					"{..1}:{..2}\n{tab}Rscript DB2_files.R {..2} {..1}"
+# 					"{..1}:{..2}\n{tab}Rscript DB2_files.R {..2} {gene_names} {..1}"
 # 				)
 # 			)
 # 	))  |>
@@ -80,7 +82,8 @@ options(scipen = 999)
 # Read arguments
 args = commandArgs(trailingOnly = TRUE)
 input_file = args[[1]]
-output_file = args[[2]]
+all_gene_names = args[[2]]
+output_file = args[[3]]
 
 output_file |> dirname() |> dir.create( showWarnings = FALSE, recursive = TRUE)
 file_id = basename(input_file) |> tools::file_path_sans_ext() |> str_split("___") %>% .[[1]] %>% .[1]
@@ -157,6 +160,21 @@ colnames(sce) = colnames(X)
 rm(X)
 gc()
 
+# Add missing genes
+missing_genes = readRDS(all_gene_names) |> setdiff(rownames(sce))
+missing_matrix =
+	HDF5RealizationSink(c(length(missing_genes),ncol(sce)), as.sparse = TRUE) |>
+	as("DelayedArray")
+
+rownames(missing_matrix) = missing_genes
+colnames(missing_matrix) = colnames(sce)
+
+missing_sce = SingleCellExperiment(list(X=missing_matrix),  colData=colData(sce))
+missing_sce@int_colData = sce@int_colData
+
+# Make cell name unique
+sce = sce |> rbind(missing_sce)
+
 sce |>	saveHDF5SummarizedExperiment(output_file, replace=TRUE)