[r] Implement as generics for SOMASparseNDArrayReader
#1458
There are no files selected for viewing
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| #' Coercion methods for SOMA classes | ||
|
|
||
| #' @importFrom arrow as_arrow_table | ||
|
There was a problem hiding this comment. Should we reexport #' @importFrom arrow as_arrow_table
#' @export
#'
arrow::as_arrow_tableIf not, these methods will be inaccessible to the end-user without |
||
| #' @export | ||
| as_arrow_table.SOMASparseNDArrayRead <- function(x){ | ||
| x$tables()$concat() | ||
| } | ||
|
|
||
| #' Coerce \link[tiledbsoma]{SOMASparseNDArrayRead} to \link{data.frame} or \link[tibble]{tibble} | ||
|
There was a problem hiding this comment. We could mention the existence of these methods in the docs for SOMASparseNDArray but I don't think we should add a description here, which results in a separate documentation entry. |
||
| #' @export | ||
| as.data.frame.SOMASparseNDArrayRead <- function(x, ...){ | ||
| as.data.frame(x$tables()$concat(), ...) | ||
| } | ||
|
|
||
| # Coerce \link[tiledbsoma]{SOMASparseNDArrayRead} to Matrix::\link[Matrix]{dgTMatrix} | ||
| setAs(from = "SOMASparseNDArrayRead", | ||
| to = "TsparseMatrix", | ||
| def = function(from) from$sparse_matrix()$concat() | ||
| ) | ||
|
Comment on lines
+26
to
+30
There was a problem hiding this comment. The R6 classes may need to be declared as an old class with methods::setOldClass("SOMASparseNDArrayRead")We may also need to import the target classes from Matrix #' @importClassesFrom Matrix TsparseMatrix CsparseMatrix RsparseMatrix
#'
NULL |
||
|
|
||
| # Coerce \link[tiledbsoma]{SOMASparseNDArrayRead} to Matrix::\link[Matrix]{dgCMatrix} | ||
| setAs(from = "SOMASparseNDArrayRead", | ||
|
There was a problem hiding this comment. We could also provide a delayed method for #' @exportS3Method SeuratObject::as.sparse
#'
as.sparse.SOMASparseNDArrayRead <- function(x, ...) {
as(x, "CsparseMatrix")
} |
||
| to = "CsparseMatrix", | ||
| def = function(from) as(as(from, "TsparseMatrix"), "CsparseMatrix") | ||
| ) | ||
|
|
||
| # Coerce \link[tiledbsoma]{SOMASparseNDArrayRead} to Matrix::\link[Matrix]{dgRMatrix} | ||
| setAs(from = "SOMASparseNDArrayRead", | ||
| to = "RsparseMatrix", | ||
| def = function(from) as(as(from, "TsparseMatrix"), "RsparseMatrix") | ||
| ) | ||
|
|
||
| #' @importFrom arrow as_arrow_table | ||
| #' @export | ||
| as_arrow_table.TableReadIter <- function(x) x$concat() | ||
|
|
||
| #' @export | ||
| as.data.frame.TableReadIter <- function(x, row.names = NULL, optional = FALSE, ...){ | ||
| as.data.frame(x$concat(), row.names = row.names, optional = optional, ...) | ||
| } | ||
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -71,7 +71,7 @@ arrow_to_dt <- function(arrlst) { | |
| } | ||
|
|
||
| ##' @noRd | ||
| to_arrow_table <- function(arrlst) { | ||
|
There was a problem hiding this comment. I could possibly make that simple list of two external pointers a simple S3 class (which I considered for the simple features like pretty printing). That may open the door for a dispatch of as_arrow_table.CLASSHERE as in your coercion utilities. Is that better? In the short term the renaming is fine but I do like these "verbs" to start with 'as' ... (We could also decide to make it There was a problem hiding this comment.
Love this idea. Almost did it myself #1461 There was a problem hiding this comment. But @pablo-gar, note that I removed the internal There was a problem hiding this comment. For correctness, let's add "proposing to remove There was a problem hiding this comment.
Come to think about it, in |
||
| check_arrow_pointers(arrlst) | ||
| arrow::as_arrow_table(arrow::RecordBatch$import_from_c(arrlst[[1]], arrlst[[2]])) | ||
| } | ||
|
|
||
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Hm. Why would we need this now when we did not before?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
No, the
Collatesecion is not necessary. My guess is it was generated when@includes were part of the code, then added as part of this PR