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Merge pull request #50 from TileDB-Inc/aaronwolen/sc-17557/adopt-czi-…
…default-layout-options Use CZI default parameters for X/obs/var
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| library(tiledbsc) | ||
| library(lobstr) | ||
| library(tiledb) | ||
| library(SeuratObject) | ||
|
|
||
| # devtools::install_github('satijalab/seurat-data') | ||
| library(SeuratData) | ||
|
|
||
| # parameters ------------------------------------------------------------------- | ||
|
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||
| # where the new arrays will be stored | ||
| array_dir <- "dev/data/arrays" | ||
|
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| # where the benchmark results will be stored | ||
| output_dir <- "dev/data/benchmarks" | ||
|
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||
| # should the new arrays be deleted after the benchmark? | ||
| clean <- FALSE | ||
|
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| # should datasets be installed if they are not already? | ||
| install_missing <- TRUE | ||
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|
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| # outputs ---------------------------------------------------------------------- | ||
|
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| # create the output file | ||
| output_metadata <- sprintf( | ||
| "%s_tiledbsc%s_tiledb%s", | ||
| format(Sys.time(),"%Y%m%d-%H%M"), | ||
| packageVersion("tiledbsc"), | ||
| packageVersion("tiledb") | ||
| ) | ||
|
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||
| output_name <- paste0("ingestion-benchmarks_", output_metadata, ".csv") | ||
|
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| output_file <- file.path(output_dir, output_name) | ||
|
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| # create parent directory using file metadata | ||
| array_dir <- file.path(array_dir, output_metadata) | ||
| dir.create(array_dir, showWarnings = FALSE, recursive = TRUE) | ||
| dir.create(output_dir, showWarnings = FALSE, recursive = TRUE) | ||
|
|
||
| # setup datasets --------------------------------------------------------------- | ||
| datasets <- AvailableData() | ||
|
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| # remove datasets with Versions < 2.0.0 to avoid the following error: | ||
| # Not a validObject(): no slot of name "images" for this object of class "Seurat" | ||
| datasets <- subset(datasets, Version >= package_version("2.0.0")) | ||
|
|
||
| # skip datasets that cause errors | ||
| blocklist <- c( | ||
| # Not a validObject(): no slot of name "images" for this object of class "Seurat" | ||
| # I believe this error is specific to datasets with Versions < 2.0.0 | ||
| "humancortexref.SeuratData", | ||
| "kidneyref.SeuratData", | ||
|
|
||
| # Datasets that are already installed but LoadData() errors with: | ||
| # Error: Could not find dataset '<>', please check manifest and try again | ||
| "bonemarrowref.SeuratData", | ||
|
|
||
| # Failed to download | ||
| "lungref.SeuratData" | ||
| ) | ||
|
|
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| # Temporarily subset | ||
| datasets <- datasets[1:min(10L, nrow(datasets)),] | ||
|
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| # setup results ---------------------------------------------------------------- | ||
|
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| # initialize results dataframe | ||
| benchmarks <- data.frame( | ||
| size_memory = numeric(), | ||
| size_rds = numeric(), | ||
| size_tiledb = numeric(), | ||
| ingest_time = numeric() | ||
| ) | ||
|
|
||
| # main ------------------------------------------------------------------------- | ||
| for (ds_name in rownames(datasets)) { | ||
| message(sprintf("Dataset: %s", ds_name)) | ||
| if (ds_name %in% blocklist) { | ||
| message(sprintf("..skipping blocklisted dataset: %s", ds_name)) | ||
| next | ||
| } | ||
|
|
||
| if (!datasets[ds_name, "Installed"]) { | ||
| skip <- FALSE | ||
| if (interactive()) { | ||
| if (menu(c("yes", "no"), sprintf("Install %s?", ds_name)) == 2) skip <- TRUE | ||
| } else { | ||
| if (!install_missing) skip <- TRUE | ||
| } | ||
|
|
||
| if (skip) { | ||
| message(sprintf("..skipping dataset not installed: %s", ds_name)) | ||
| next | ||
| } | ||
|
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| message(sprintf("..installing dataset '%s'", ds_name)) | ||
| install_worked <- try(InstallData(ds_name), silent = TRUE) | ||
| if (inherits(install_worked, "try-error")) { | ||
| message(sprintf("..failed to install dataset '%s'", ds_name)) | ||
| next | ||
| } | ||
| } | ||
|
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| message("..loading dataset") | ||
| ds <- LoadData(ds_name) | ||
|
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| uri <- file.path(array_dir, ds_name) | ||
| message(sprintf("..ingesting data into '%s'", uri)) | ||
|
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| ingest_start <- Sys.time() | ||
| scgroup <- SCGroup$new(uri = uri) | ||
| scgroup$from_seurat_assay( | ||
| object = ds[[DefaultAssay(ds)]], | ||
| obs = ds[[]] | ||
| ) | ||
|
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| benchmarks[ds_name, ] <- list( | ||
| size_memory = as.numeric(obj_size(ds)), | ||
| size_rds = tiledb_vfs_dir_size(system.file("data", package = ds_name)), | ||
| size_tiledb = tiledb_vfs_dir_size(uri), | ||
| ingest_time = as.numeric(difftime(Sys.time(), ingest_start, units = "secs")) | ||
| ) | ||
|
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| # write each time to avoid losing data on failures | ||
| write.csv(benchmarks, file = output_file, quote = FALSE) | ||
|
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| if (clean) { | ||
| message(sprintf("..cleaning dataset '%s'", ds_name)) | ||
| tiledb_vfs_remove_dir(uri) | ||
| } | ||
| } |
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