hd5f format of available Allen Brain Atlas mouse data

[rbutleriii]

Hello,

When trying to use hd5f format data from the AIBS mouse dataset, I am running into issues getting it into the right format and I am wondering if anyone else has encountered this. Similar to #732.

> mtx = H5File$new("expression_matrix.hdf5", mode='r')
> mtx
Class: H5File
Filename: /oak/stanford/scg/lab_flongo/reference/allen_brain_atlas/mouse_cortex/expression_matrix.hdf5
Access type: H5F_ACC_RDONLY
Listing:
 name  obj_type dataset.dims dataset.type_class
 data H5I_GROUP         <NA>               <NA>
> mtx[['data']]
Class: H5Group
Filename: /oak/stanford/scg/lab_flongo/reference/allen_brain_atlas/mouse_cortex/expression_matrix.hdf5
Group: /data
Listing:
    name    obj_type    dataset.dims dataset.type_class
  counts H5I_DATASET 1169320 x 31053        H5T_INTEGER
    gene H5I_DATASET           31053         H5T_STRING
 samples H5I_DATASET         1169320         H5T_STRING
   shape H5I_DATASET               2        H5T_INTEGER
> feature_matrix = Matrix::sparseMatrix(
+   i = seq(mtx[['data/shape']][1]),
+   j = seq(mtx[['data/shape']][2]),
+   x = mtx[['data/counts']][],
+   dimnames = list(
+     mtx[['data/samples']][],
+     mtx[['data/gene']][]
+   ),
+   dims = mtx[['data/shape']][]
+ )
Error in args_regularity_evaluation(args = args, ds_dims = simple_extent$dims,  :
  Number of arguments not equal to number of dimensions: 1 vs. 2