Export to spring issue (AttributeError: 'numpy.ndarray' object has no attribute 'tocsc')

Question

Export to spring issue (AttributeError: 'numpy.ndarray' object has no attribute 'tocsc')

sfortma2 opened this issue 4 years ago · comments

Hi,

I am having an issue exporting my h5ad file to spring for visualization. I have been following the spring export tutorial but every time I try to run sc.export_to.spring_project I get the following error:

sc.export_to.spring_project(adata1, '/home/seth/anaconda3/write', 'draw_graph')
Writing subplot to /home/seth/anaconda3
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-9-656bbf38658a> in <module>
----> 1 sc.export_to.spring_project(adata1, '/home/seth/anaconda3/write', 'draw_graph', cell_groupings='louvain_r0.8_sub')

~/anaconda3/envs/ddocent_env/lib/python3.7/site-packages/scanpy/_exporting.py in spring_project(adata, project_dir, embedding_method, subplot_name, cell_groupings, custom_color_tracks, total_counts_key, overwrite)
    101     # Ideally, all genes will be written from adata.raw
    102     if adata.raw is not None:
--> 103         E = adata.raw.X.tocsc()
    104         gene_list = list(adata.raw.var_names)
    105     else:

AttributeError: 'numpy.ndarray' object has no attribute 'tocsc'

I can't seem to get around this error. I tried posting in the scanpy github page but received no responses. Any help would be greatly appreciated!

Thanks,
Seth

Caleb Weinreb · Answer 1 · Thu Feb 20 2020 22:15:21 GMT+0800 (China Standard Time)

Hi, The problem is that "adata.raw.X" is stored as a numpy array and not as a sparse matrix. I'm not sure the proper way to fix this in scanpy, but as a hack you can just do "adata.raw.X = scipy.sparse.csc_matrix(adata.raw.X)

…

On Tue, Feb 18, 2020 at 9:20 PM sfortma2 ***@***.***> wrote: Hi, I am having an issue exporting my h5ad file to spring for visualization. I have been following the spring export tutorial <https://github.com/theislab/scanpy_usage/tree/master/171111_SPRING_export> but every time I try to run sc.export_to.spring_project I get the following error: sc.export_to.spring_project(adata1, '/home/seth/anaconda3/write', 'draw_graph') Writing subplot to /home/seth/anaconda3 --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-9-656bbf38658a> in <module> ----> 1 sc.export_to.spring_project(adata1, '/home/seth/anaconda3/write', 'draw_graph', cell_groupings='louvain_r0.8_sub') ~/anaconda3/envs/ddocent_env/lib/python3.7/site-packages/scanpy/_exporting.py in spring_project(adata, project_dir, embedding_method, subplot_name, cell_groupings, custom_color_tracks, total_counts_key, overwrite) 101 # Ideally, all genes will be written from adata.raw 102 if adata.raw is not None: --> 103 E = adata.raw.X.tocsc() 104 gene_list = list(adata.raw.var_names) 105 else: AttributeError: 'numpy.ndarray' object has no attribute 'tocsc' I can't seem to get around this error. I tried posting in the scanpy github page but received no responses. Any help would be greatly appreciated! Thanks, Seth — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#19?email_source=notifications&email_token=ABO45MQL5OZWPNVQ4DVA2HLRDSJPHA5CNFSM4KXQJUAKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IOP4S7Q>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MT2NCBEDFOSJZMUHDLRDSJPHANCNFSM4KXQJUAA> .