R/seqFISH.R

In waldronlab/SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

#' Single-cell spatial + Gene Expression
#'
#' @description seqFISH function assembles data on-the-fly from `ExperimentHub`
#'   to provide a
#'   [`MultiAssayExperiment`][MultiAssayExperiment::MultiAssayExperiment-class]
#'   container. Actually the `DataType` argument provides access to the
#'   available datasets associated to the package.
#'
#' @details seq FISH data are a combination of single cell spatial coordinates
#'   and transcriptomics for a few hundreds of genes. seq-FISH data can be
#'   combined for example with scRNA-seq data to unveil multiple aspects of
#'   cellular behaviour based on their spatial organization and transcription.
#'
#' Available datasets are:
#' * mouse_visual_cortex: combination of seq-FISH data as obtained from Zhu
#' et al. (2018) and scRNA-seq data as obtained from Tasic et al. (2016),
#' Version 1.0.0 returns the full scRNA-seq data matrix, while version 2.0.0
#' returns the processed and subsetted scRNA-seq data matrix (produced for
#' the Mathematical Frameworks for Integrative Analysis of Emerging
#' Biological Data Types 2020 Workshop) The returned seqFISH data are always
#' the processed ones for the same workshop. Additionally, cell types
#' annotations are available in the `colData` through the `class` column in
#' the seqFISH `assay`.
#'     * scRNA_Counts - Tasic scRNA-seq gene count matrix
#'     * scRNA_Labels - Tasic scRNA-seq cell labels
#'     * seqFISH_Coordinates - Zhu seq-FISH spatial coordinates
#'     * seqFISH_Counts - Zhu seq-FISH gene counts matrix
#'     * seqFISH_Labels - Zhu seq-FISH cell labels
#'
#' @inheritParams scNMT
#'
#' @param DataType `character(1)` indicating the identifier of the dataset to
#'     retrieve.  (default "mouse_visual_cortex")
#'
#' @param modes `character()` The assay types or modes of data to obtain these
#'     include seq-FISH and scRNA-seq data by default.
#'
#' @return A
#'   [`MultiAssayExperiment`][MultiAssayExperiment::MultiAssayExperiment-class]
#'   of seq-FISH data
#'
#' @author Dario Righelli <dario.righelli <at> gmail.com>
#'
#' @importFrom SpatialExperiment SpatialExperiment
#' @importFrom SingleCellExperiment SingleCellExperiment
#' @importFrom S4Vectors DataFrame
#'
#' @examples
#'
#' seqFISH(DataType = "mouse_visual_cortex", modes = "*", version = "2.0.0",
#'     dry.run = TRUE)
#'
#' @export
seqFISH <-
    function(
        DataType="mouse_visual_cortex", modes="*", version,
        dry.run=TRUE, verbose=TRUE, ...
    )
{
    ess_list <- .getResourcesList(prefix = "seqfish_", datatype = DataType,
        modes = modes, version = version, dry.run = dry.run,
        verbose = verbose, ...)

    if (dry.run) { return(ess_list) }

    modes_list <- ess_list[["experiments"]]

    switch(DataType,
        "mouse_visual_cortex" = {
            mae <- .mouse_visual_cortex(modes_list=modes_list,
                                        version=version)
        },
        ## Add here other seqFISH datasets based on DataType identifier
        {
            stop("Unrecognized seqFISH dataset name")
        }
    )

    return(mae)
}

.mouse_visual_cortex <- function(modes_list, version)
{
    res <- paste0("scRNA",
        if (identical(version, "1.0.0")) "_Full" else "",
        "_", c("Counts", "Labels")
    )

    ## discrepancy between labels in counts and colData
    counts <- as.matrix(modes_list[[res[1]]])
    ## rowData is duplicate of rownames [removed]
    coldata <- modes_list[[res[2]]]
    vIDs <- intersect(rownames(coldata), colnames(counts))
    counts <- counts[, vIDs]
    coldata <- coldata[vIDs, ]

    sce <- SingleCellExperiment::SingleCellExperiment(
        colData=coldata,
        assays=S4Vectors::SimpleList(counts=counts)
    )

    se <- SpatialExperiment::SpatialExperiment(
        rowData=rownames(modes_list$seqFISH_Counts),
        colData=modes_list$seqFISH_Labels,
        assays=S4Vectors::SimpleList(
            counts=as.matrix(modes_list$seqFISH_Counts)),
        spatialData=DataFrame(modes_list$seqFISH_Coordinates),
        spatialCoordsNames=c("x", "y"))

    MultiAssayExperiment(
        experiments = list(seqFISH = se, scRNAseq = sce)
    )
}