maximilianh
commented
5 years ago Ah. This happens when the object contains more than two dimensions. In this case, they calculated umap with many dimensions. Apparently only for a few tissues. Fixed now in 0.5.45. Thanks!
On Wed, Jul 31, 2019 at 11:07 PM Matt Speir notifications@github.com wrote:
When I try importing one of the new Tabula Muris Senis h5ad files, I get the following error:
INFO:root:Writing UMAP coords to tms-brain-myeloid-facs/umap_coords.tsv Traceback (most recent call last): File "/cluster/home/mspeir/miniconda3/bin/cbImportScanpy", line 10, in
sys.exit(cbImportScanpyCli()) File "/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/cellbrowser/convert.py", line 522, in cbImportScanpyCli markerField=markerField) File "/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 3278, in scanpyToCellbrowser writeAnndataCoords(adata, layoutCode, path, layoutCode, layoutName, coordDescs) File "/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 3098, in writeAnndataCoords fa2_coord.columns=['x','y'] File "/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/pandas/core/generic.py", line 4385, in setattr return object.setattr(self, name, value) File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.set File "/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/pandas/core/generic.py", line 645, in _set_axis self._data.set_axis(axis, labels) File "/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/pandas/core/internals.py", line 3323, in set_axis 'values have {new} elements'.format(old=old_len, new=new_len)) ValueError: Length mismatch: Expected axis has 12 elements, new values have 2 elements Some files (e.g. Bladder_droplet.h5ad and Bladder_facs.h5ad) work fine, but running it for this dataset (Brain_Myeloid_facs.h5ad) results in an error.
Command:
cbImportScanpy -i orig/Brain_Myeloid_facs.h5ad -o tms-brain-myeloid-facs -n tms-brain-myeloid-facs
Data location:
/hive/data/inside/cells/datasets/tabula-muris-senis
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When I try importing one of the new Tabula Muris Senis h5ad files, I get the following error:
Some files (e.g. Bladder_droplet.h5ad and Bladder_facs.h5ad) work fine, but running it for this dataset (Brain_Myeloid_facs.h5ad) results in an error.
Command:
Data location: