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Can not write array and dgeMatrix objects #198

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ToryDeng opened this issue Nov 13, 2024 · 1 comment
Open

Can not write array and dgeMatrix objects #198

ToryDeng opened this issue Nov 13, 2024 · 1 comment

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@ToryDeng
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I am unable to write objects of type array and dgeMatrix to .h5ad files. Here is an example R script demonstrating this issue:

adata <- generate_dataset(format = "AnnData")
adata$uns <- list(arr=array(c(1:30),dim = c(3,2,5)))
write_h5ad(adata, "test_adata.h5ad")
warnings()
Warning messages:
1: In value[[3L]](cond) :
  Could not write element 'layers/numeric_dense' of type 'dgeMatrix':
unknown type
2: In value[[3L]](cond) :
  Could not write element 'layers/numeric_dense_with_nas' of type 'dgeMatrix':
unknown type
3: In value[[3L]](cond) :
  Could not write element 'layers/integer_dense' of type 'dgeMatrix':
unknown type
4: In value[[3L]](cond) :
  Could not write element 'layers/integer_dense_with_nas' of type 'dgeMatrix':
unknown type
5: In value[[3L]](cond) :
  Could not write element 'obsm/numeric_dense' of type 'dgeMatrix':
unknown type
6: In value[[3L]](cond) :
  Could not write element 'obsm/numeric_dense_with_nas' of type 'dgeMatrix':
unknown type
7: In value[[3L]](cond) :
  Could not write element 'obsm/integer_dense' of type 'dgeMatrix':
unknown type
8: In value[[3L]](cond) :
  Could not write element 'obsm/integer_dense_with_nas' of type 'dgeMatrix':
unknown type
9: In value[[3L]](cond) :
  Could not write element 'varm/numeric_dense' of type 'dgeMatrix':
unknown type
10: In value[[3L]](cond) :
  Could not write element 'varm/numeric_dense_with_nas' of type 'dgeMatrix':
unknown type
11: In value[[3L]](cond) :
  Could not write element 'varm/integer_dense' of type 'dgeMatrix':
unknown type
12: In value[[3L]](cond) :
  Could not write element 'varm/integer_dense_with_nas' of type 'dgeMatrix':
unknown type
13: In value[[3L]](cond) :
  Could not write element 'obsp/numeric_dense' of type 'dgeMatrix':
unknown type
14: In value[[3L]](cond) :
  Could not write element 'obsp/numeric_dense_with_nas' of type 'dgeMatrix':
unknown type
15: In value[[3L]](cond) :
  Could not write element 'obsp/integer_dense' of type 'dgeMatrix':
unknown type
16: In value[[3L]](cond) :
  Could not write element 'obsp/integer_dense_with_nas' of type 'dgeMatrix':
unknown type
17: In value[[3L]](cond) :
  Could not write element 'varp/numeric_dense' of type 'dgeMatrix':
unknown type
18: In value[[3L]](cond) :
  Could not write element 'varp/numeric_dense_with_nas' of type 'dgeMatrix':
unknown type
19: In value[[3L]](cond) :
  Could not write element 'varp/integer_dense' of type 'dgeMatrix':
unknown type
20: In value[[3L]](cond) :
  Could not write element 'varp/integer_dense_with_nas' of type 'dgeMatrix':
unknown type
21: In value[[3L]](cond) : Could not write element 'uns/arr' of type 'array':
argument is not a matrix

Is there a way to resolve this issue, or is this functionality not yet implemented in anndataR?

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@ToryDeng and others