CI
72b5c7c839
Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-6h5zv
Source commit: 280b21fc21
Source message: deploy: 6840f3802d04d96d44f29d3cdbd31c62d144b14d
35 lines
934 B
R
35 lines
934 B
R
library(SpatialExperimentIO)
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### VIASH START
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par <- list(
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input = "resources_test/cosmx/Lung5_Rep2_tiny",
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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("NegPrb", "Negative", "SystemControl", "FalseCode"),
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output = "spe_cosmx_test.rds"
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)
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### VIASH END
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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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spe <- readCosmxSXE(
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dirName = par$input,
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returnType = "SPE",
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countMatPattern = "exprMat_file.csv",
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metaDataPattern = "metadata_file.csv",
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coordNames = c("CenterX_global_px", "CenterY_global_px"),
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addFovPos = par$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$alternative_experiment_features
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)
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saveRDS(spe, file = par$output)
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