reannotate difficult cells

Author: stemangiola

dev/reannotate_cd4.R

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+library(scuttle)
+library(celldex)
+library(SingleR)
+library(BiocParallel)
+library(HCAquery)
+library(SingleCellExperiment)
+library(tidySingleCellExperiment)
+library(digest)
+library(openssl)
+library(stringr)
+library(HDF5Array)
+monocyte_reference = celldex::MonacoImmuneData()
+
+
+readRDS("/vast/projects/RCP/human_cell_atlas/metadata.rds") |>
+	filter(.cell %in% (
+		readRDS("dev/curated_annotation.rds") |>
+			filter(cell_type_harmonised=="cd4 t") |>
+			pull(.cell)
+	)) |>
+	unite("file_id_db", c(file_id, cell_type), remove = FALSE) |>
+	mutate(file_id_db = file_id_db |> md5() |> as.character()) |>
+
+	get_SingleCellExperiment("/vast/projects/RCP/human_cell_atlas/splitted_DB2_data") |>
+
+	# Annotate
+	logNormCounts(assay.type = "X") |>
+	SingleR(
+		ref = monocyte_reference,
+		assay.type.test=1,
+		labels = monocyte_reference$label.fine
+	) |>
+	saveRDS("reannotate_cd4.rds")

dev/reannotate_cd8.R

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+library(scuttle)
+library(celldex)
+library(SingleR)
+library(BiocParallel)
+library(HCAquery)
+library(SingleCellExperiment)
+library(tidySingleCellExperiment)
+library(digest)
+library(openssl)
+library(stringr)
+library(HDF5Array)
+monocyte_reference =celldex::MonacoImmuneData()
+
+
+readRDS("/vast/projects/RCP/human_cell_atlas/metadata.rds") |>
+	filter(.cell %in% (
+		readRDS("dev/curated_annotation.rds") |>
+			filter(cell_type_harmonised=="cd8 t") |>
+			pull(.cell)
+	)) |>
+	unite("file_id_db", c(file_id, cell_type), remove = FALSE) |>
+	mutate(file_id_db = file_id_db |> md5() |> as.character()) |>
+
+	get_SingleCellExperiment("/vast/projects/RCP/human_cell_atlas/splitted_DB2_data") |>
+
+	# Annotate
+	logNormCounts(assay.type = "X") |>
+
+	SingleR(
+		ref = monocyte_reference,
+		assay.type.test=1,
+		labels = monocyte_reference$label.fine
+	) |>
+	saveRDS("reannotate_cd8.rds")

dev/reannotate_monocytes.R

@@ -0,0 +1,34 @@
+library(scuttle)
+library(celldex)
+library(SingleR)
+library(BiocParallel)
+library(HCAquery)
+library(SingleCellExperiment)
+library(tidySingleCellExperiment)
+library(digest)
+library(openssl)
+library(stringr)
+library(HDF5Array)
+monocyte_reference =celldex::MonacoImmuneData()
+
+
+
+readRDS("/vast/projects/RCP/human_cell_atlas/metadata.rds") |>
+	filter(.cell %in% (
+		readRDS("dev/curated_annotation.rds") |>
+			filter(cell_type_harmonised=="monocytes") |>
+			pull(.cell)
+	)) |>
+	unite("file_id_db", c(file_id, cell_type), remove = FALSE) |>
+	mutate(file_id_db = file_id_db |> md5() |> as.character()) |>
+
+	get_SingleCellExperiment("/vast/projects/RCP/human_cell_atlas/splitted_DB2_data") |>
+
+	# Annotate
+	logNormCounts(assay.type = "X") |>
+	SingleR(
+		ref = monocyte_reference,
+		assay.type.test=1,
+		labels = monocyte_reference$label.fine
+	) |>
+	saveRDS("reannotate_monocytes.rds")