CI
c6296af264
Build pipeline: test-vsh-ci-build-template-qlrkg
Source commit: 3b5314b60d
Source message: update changelog
63 lines
1.5 KiB
R
63 lines
1.5 KiB
R
library(SpatialExperimentIO)
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### VIASH START
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par <- list(
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input = "resources_test/cosmx/test2.zip",
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add_tx_path = TRUE,
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add_polygon_path = FALSE,
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add_fov_positions = TRUE,
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alternative_experiment_features = c(
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"NegPrb", "Negative", "SystemControl", "FalseCode"
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),
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output = "spe_cosmx_test.rds"
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)
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meta <- list(
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resources_dir = "src/utils/"
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)
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### VIASH END
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source(paste0(meta$resources_dir, "/unzip_archived_folder.R"))
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cat("Reading input data...")
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if (tools::file_ext(par$input) == "zip") {
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expected_file_patterns <- c(
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"*.csv",
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"*.parquet"
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)
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tmp_dir <- extract_selected_files(
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par$input,
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members = expected_file_patterns
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)
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cosmx_output_bundle <- file.path(
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tmp_dir,
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tools::file_path_sans_ext(basename(par$input))
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)
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} else {
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cosmx_output_bundle <- par$input
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}
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cat("Setting parameters...")
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if (par$add_polygon_path == FALSE && par$add_tx_path == FALSE) {
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add_parquet_paths <- FALSE
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} else {
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add_parquet_paths <- TRUE
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}
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cat("Converting to SpatialExperiment...")
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spe <- readCosmxSXE(
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dirName = cosmx_output_bundle,
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returnType = "SPE",
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countMatPattern = "exprMat_file.csv",
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metaDataPattern = "metadata_file.csv",
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coordNames = c("CenterX_global_px", "CenterY_global_px"),
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addFovPos = par$add_fov_positions,
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fovPosPattern = "fov_positions_file.csv",
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addParquetPaths = add_parquet_paths,
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addPolygon = par$add_polygon_path,
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addTx = par$add_tx_path,
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altExps = par$alternative_experiment_features
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)
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cat("Saving output...")
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saveRDS(spe, file = par$output)
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