## ----setup, echo = FALSE, results = "hide", message = FALSE------------------- require(knitr) library(BiocStyle) opts_chunk$set(error = FALSE, message = FALSE, warning = FALSE) ## ----read--------------------------------------------------------------------- library(zellkonverter) # Obtaining an example H5AD file. example_h5ad <- system.file("extdata", "krumsiek11.h5ad", package = "zellkonverter") readH5AD(example_h5ad) ## ----write-------------------------------------------------------------------- library(scRNAseq) sce_zeisel <- ZeiselBrainData() out_path <- tempfile(pattern = ".h5ad") writeH5AD(sce_zeisel, file = out_path) ## ----convert------------------------------------------------------------------ library(basilisk) library(scRNAseq) seger <- SegerstolpePancreasData() roundtrip <- basiliskRun(fun = function(sce) { # Convert SCE to AnnData: adata <- SCE2AnnData(sce) # Maybe do some work in Python on 'adata': # BLAH BLAH BLAH # Convert back to an SCE: AnnData2SCE(adata) }, env = zellkonverterAnnDataEnv(), sce = seger) ## ----anndata-deps------------------------------------------------------------- AnnDataDependencies() ## ----anndata-deps-old--------------------------------------------------------- AnnDataDependencies(version = "0.7.6") ## ----verbose------------------------------------------------------------------ readH5AD(example_h5ad, verbose = TRUE) ## ----verbose-set, eval = FALSE------------------------------------------------ # # This is not run here # setZellkonverterVerbose(TRUE) ## ----------------------------------------------------------------------------- sessionInfo()