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Convert between Matrix and scipy sparse representations

Source: R/py_utils.R
scipy_sparse.Rd

Convert between R Matrix sparse matrix representation and python scipy sparse formats. Inspired by the implementation in nmslibR. Currently compatible classes:

  • to_scipy_sparse(): matrix, dgCMatrix, dgRMatrix, dgTMatrix

  • from_scipy_sparse(): scipy.sparse._csr.csr_matrix, scipy.sparse._csc.csc_matrix

Usage

to_scipy_sparse(x, format = c("C", "R"), transpose = FALSE, ...)

from_scipy_sparse(x, format = c("C", "R"), transpose = FALSE, ...)

Arguments

x

matrix-like object to convert

format

character. Either "C" for Compressed Sparse Column or "R" for Compressed Sparse Row matrix representations

transpose

whether to transpose the matrix. default is FALSE

...

additional params to pass to scipy.sparse.cs*_matrix() or Matrix::sparseMatrix depending on which output is desired.

Value

scipy or Matrix sparse representation depending on 'to' or 'from' respectively

Examples

# example data
m <- matrix(data = 0L, nrow = 400, ncol = 300)
m[sample(400, 100), sample(300, 100)] <- runif(100, max = 10)
dgc <- Matrix::rsparsematrix(nrow = 400L, ncol = 300L, density = 0.1)

# some conversions
py_m_c <- to_scipy_sparse(m, format = "C")
#> Error in py_module_import(module, convert = convert): ModuleNotFoundError: No module named 'scipy'
#> Run `reticulate::py_last_error()` for details.
py_m_r_t <- to_scipy_sparse(m, format = "R", transpose = TRUE)
#> Error in py_module_import(module, convert = convert): ModuleNotFoundError: No module named 'scipy'
#> Run `reticulate::py_last_error()` for details.

py_dgc_c <- to_scipy_sparse(dgc, format = "C")
#> Error in py_module_import(module, convert = convert): ModuleNotFoundError: No module named 'scipy'
#> Run `reticulate::py_last_error()` for details.
py_dgc_r <- to_scipy_sparse(dgc, format = "R")
#> Error in py_module_import(module, convert = convert): ModuleNotFoundError: No module named 'scipy'
#> Run `reticulate::py_last_error()` for details.

dgc_revert <- from_scipy_sparse(py_dgc_c, format = "C")
#> Error in eval(expr, envir, enclos): object 'py_dgc_c' not found
dgr_revert <- from_scipy_sparse(py_dgc_c, format = "R")
#> Error in eval(expr, envir, enclos): object 'py_dgc_c' not found
identical(dgc, dgc_revert)
#> Error in eval(expr, envir, enclos): object 'dgc_revert' not found