TO_scipy_sparse function

conversion of an R sparse matrix to a scipy sparse matrix

TO_scipy_sparse(R_sparse_matrix)

Arguments

• R_sparse_matrix: an R sparse matrix. Acceptable input objects are either a dgCMatrix or a dgRMatrix.

Details

This function allows the user to convert either an R dgCMatrix or a dgRMatrix to a scipy sparse matrix (scipy.sparse.csc_matrix or scipy.sparse.csr_matrix). This is useful because the RGF package accepts besides an R dense matrix also python sparse matrices as input.

The dgCMatrix class is a class of sparse numeric matrices in the compressed, sparse, column-oriented format. The dgRMatrix class is a class of sparse numeric matrices in the compressed, sparse, row-oriented format.

Examples

try({
    if (reticulate::py_available(initialize = FALSE)) {
        if (reticulate::py_module_available("scipy")) {

            if (Sys.info()["sysname"] != 'Darwin') {

                library(RGF)

                # 'dgCMatrix' sparse matrix
                #--------------------------

                data = c(1, 0, 2, 0, 0, 3, 4, 5, 6)

                dgcM = Matrix::Matrix(
                    data = data
                    , nrow = 3
                    , ncol = 3
                    , byrow = TRUE
                    , sparse = TRUE
                )

                print(dim(dgcM))

                res = TO_scipy_sparse(dgcM)

                print(res$shape)

                # 'dgRMatrix' sparse matrix
                #--------------------------

                dgrM = as(dgcM, "RsparseMatrix")

                print(dim(dgrM))

                res_dgr = TO_scipy_sparse(dgrM)

                print(res_dgr$shape)
            }
        }
    }
}, silent = TRUE)

References

https://stat.ethz.ch/R-manual/R-devel/library/Matrix/html/dgCMatrix-class.html, https://stat.ethz.ch/R-manual/R-devel/library/Matrix/html/dgRMatrix-class.html, https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csc_matrix.html#scipy.sparse.csc_matrix