## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>",
                      error = FALSE, warning = FALSE, message = FALSE)

## ----live-demo----------------------------------------------------------------
library(BiocDuckDB)
library(DuckDBArray)
library(Matrix)
library(scuttle)

set.seed(1L)
m <- as(Matrix(rpois(2000 * 400, lambda = 0.3), nrow = 2000, ncol = 400,
               sparse = TRUE), "dgCMatrix")
rownames(m) <- paste0("Gene", seq_len(nrow(m)))
colnames(m) <- paste0("Cell", seq_len(ncol(m)))

path <- tempfile()
writeParquet(t(m), path)
mt <- t(m)
mat <- DuckDBMatrix(path, datacol = "value",
    keycols = list(index2 = setNames(seq_len(ncol(mt)), colnames(mt)),
                   index1 = setNames(seq_len(nrow(mt)), rownames(mt))),
    dimtbls = createDimTables(mt))

## same answer, one in memory and one queried from disk
qc_mem <- perCellQCMetrics(m)
qc_ddb <- perCellQCMetrics(mat)
all.equal(qc_mem$sum, qc_ddb$sum)

## ----results, echo=FALSE, results='asis'--------------------------------------
helper <- system.file("scripts", "make_timings_table.R", package = "BiocDuckDB")
if (nzchar(helper)) {
    source(helper)
    res <- load_vignette_timings()
} else {
    res <- NULL
}
if (is.null(res)) {
    cat("_Precomputed benchmark results are not available in this build; ",
        "generate them with `inst/scripts/run_scran_scuttle_benchmarks.R`._\n", sep = "")
} else {
    print(make_timings_table(
        caption = "Elapsed seconds per operation. Speedups > 1 favor DuckDB.",
        results = res))
    cat("\n\n")
    timings_config_note(res)
}

## ----sessioninfo--------------------------------------------------------------
sessionInfo()