Description Usage Arguments Details Value Author(s) See Also Examples
Conversion between Python AnnData objects and SingleCellExperiment objects.
1 2 3 | AnnData2SCE(adata, skip_assays = FALSE, hdf5_backed = TRUE)
SCE2AnnData(sce, X_name = NULL, skip_assays = FALSE)
|
adata |
A reticulate reference to a Python AnnData object. |
skip_assays |
Logical scalar indicating whether to skip conversion of
any assays in |
hdf5_backed |
Logical scalar indicating whether HDF5-backed matrices
in |
sce |
A SingleCellExperiment object. |
X_name |
Name of the assay to use as the primary matrix ( |
These functions assume that an appropriate Python environment has already been loaded. As such, they are largely intended for developer use, most typically inside a basilisk context.
The conversion is not entirely lossless. The current mapping is shown below (also at https://tinyurl.com/AnnData2SCE):
In SCE2AnnData()
, matrices are converted to a numpy-friendly format.
Sparse matrices are converted to dgCMatrix objects while all
other matrices are converted into ordinary matrices. If skip_assays = TRUE
,
empty sparse matrices are created instead and the user is expected to fill in
the assays on the Python side.
For AnnData2SCE()
, a warning is raised if there is no corresponding R format
for a matrix in the AnnData object, and an empty sparse matrix is created
instead as a placeholder. If skip_assays = NA
, no warning is emitted
but variables are created in the int_metadata()
of the output to specify
which assays were skipped.
If skip_assays = TRUE
, empty sparse matrices are created for all assays,
regardless of whether they might be convertible to an R format or not.
In both cases, the user is expected to fill in the assays on the R side,
see readH5AD()
for an example.
We attempt to convert between items in the SingleCellExperiment
metadata()
slot and the AnnData
uns
slot. If an item cannot be
converted a warning will be raised.
Values stored in the varm
slot of an AnnData
object are stored in a
column of rowData()
in a SingleCellExperiment
as a DataFrame of matrices. No attempt is made to transfer this
information when converting from SingleCellExperiment to
AnnData
.
AnnData2SCE()
will return a SingleCellExperiment
containing the equivalent data from adata
.
SCE2AnnData()
will return a reticulate reference to an AnnData object
containing the content of sce
.
Luke Zappia
Aaron Lun
writeH5AD()
and readH5AD()
for dealing directly with H5AD files.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | if (requireNamespace("scRNAseq", quietly = TRUE)) {
library(basilisk)
library(scRNAseq)
seger <- SegerstolpePancreasData()
# These functions are designed to be run inside
# a specified Python environment
roundtrip <- basiliskRun(fun = function(sce) {
# Convert SCE to AnnData:
adata <- SCE2AnnData(sce)
# Maybe do some work in Python on 'adata':
# BLAH BLAH BLAH
# Convert back to an SCE:
AnnData2SCE(adata)
}, env = zellkonverter:::anndata_env, sce = seger)
}
|
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