R/sce2adata.R

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

#' Coverts SingleCellExperiment object from R to anndata.AnnData object in
#' Python
#'
#' The AnnData object here can be saved to .h5ad file and read into Python
#' interactive console. Mostly used senario is when you want to apply
#' reticulated Python function, which only works with an anndata.AnnData object.
#' @param SCE A SingleCellExperiment object.
#' @param useAssay Character, default `"counts"`. The name of assay of
#' interests that will be set as the primary matrix of the output AnnData.
#' Available options can be listed by `assayNames(SCE)`. Thee primary matrix
#' will be saved in `adata$X`, Other assays will be stored in `adata$obsm`
#' together with the low-dimension representations (for now).
#' @return A Python anndata.AnnData object
.sce2adata <- function(SCE, useAssay = 'counts') {
    # Transfer SCE object back to AnnData
    # Argument check first
    stopifnot(inherits(SCE, "SingleCellExperiment"))

    # Extract information that correspond to AnnData structure
    X <- t(SummarizedExperiment::assay(SCE, useAssay))
    AnnData <- sc$AnnData(X = X)
    obs <- as.data.frame(SummarizedExperiment::colData(SCE))
    if(length(obs) > 0){
        AnnData$obs = obs
    } else {
        AnnData$obs_names <- colnames(SCE)
    }
    var <- as.data.frame(SummarizedExperiment::rowData(SCE))
    if(length(var) > 0){
        AnnData$var = var
    } else {
        AnnData$var_names <- rownames(SCE)
    }
    # uns  <- S4Vectors::metadata(SCE)
    # if(length(uns) > 0){
    #     AnnData$uns <- uns
    # }
    obsmNames <- SingleCellExperiment::reducedDimNames(SCE)
    if(length(obsmNames) > 0){
        for (i in seq_along(obsmNames)) {
            AnnData$obsm$'__setitem__'(obsmNames[i],
                            SingleCellExperiment::reducedDim(SCE, obsmNames[i]))
        }
    }

    # Furthermore, the other assays will for now also be saved to .layers
    allAssayNames <- SummarizedExperiment::assayNames(SCE)
    for (i in seq_along(allAssayNames)) {
        oneName <- allAssayNames[i]
        if (!oneName == useAssay) {
            AnnData$layers$'__setitem__'(oneName,
                                       t(SummarizedExperiment::assay(SCE,
                                                                     oneName)))
        }
    }
    return(AnnData)
}