Writing and reading h5ad files from R using the zellkonverter Bioconductor R package

read_write_h5ad.R

libraries = c("zellkonverter", "SingleCellExperiment")
for (lib in libraries) {
  suppressPackageStartupMessages(library(lib, character.only = TRUE,
                                         quietly = TRUE))
} 

# dummy SingleCellExperiment
ncells <- 100
u <- matrix(rpois(20000, 5), ncol = ncells)
v <- log2(u + 1)

pca <- matrix(runif(ncells*5), ncells)
tsne <- matrix(rnorm(ncells*2), ncells)

sce <- SingleCellExperiment(assays = list(counts = u, logcounts = v),
                            reducedDims = SimpleList(PCA = pca, tSNE = tsne))
sce

out_path <- tempfile(fileext = ".h5ad")

# When first run, this will instantiate a conda environment for zellkonverter
writeH5AD(sce, file = out_path, verbose = TRUE)

readH5AD(out_path, verbose = TRUE)