TypeError when using the exporting.spring_project function
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Description
I've been trying to export my data to SPRING using the external export feature. I do all my processing in Seurat and then export a loom file to be read in scanpy and export to SPRING. I've been however getting the below error.
The notebook with the code and the loom file can be found here: https://github.com/tejas-j/seurat2spring
Is there a better way to achieve what I'm trying to do (data -> Seurat -> scanpy -> SPRING)
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-13-3b0044b18ade> in <module>
1 import time
2 t0 = time.time()
----> 3 sce.exporting.spring_project(data, './pbmc3k', 'draw_graph', subplot_name='force1', overwrite=True)
4 print(time.time() - t0)
~/miniconda2/envs/py36/lib/python3.6/site-packages/scanpy/_exporting.py in spring_project(adata, project_dir, embedding_method, subplot_name, cell_groupings, custom_color_tracks, total_counts_key, overwrite)
157 # Write continuous colors
158 continuous_extras['Uniform'] = np.zeros(E.shape[0])
--> 159 write_color_tracks(continuous_extras, subplot_dir / 'color_data_gene_sets.csv')
160
161 # Create and write a dictionary of color profiles to be used by the visualizer
~/miniconda2/envs/py36/lib/python3.6/site-packages/scanpy/_exporting.py in write_color_tracks(ctracks, fname)
301 out = []
302 for name,score in ctracks.items():
--> 303 line = name + ',' + ','.join(['%.3f' %x for x in score])
304 out += [line]
305 out = sorted(out,key=lambda x: x.split(',')[0])
~/miniconda2/envs/py36/lib/python3.6/site-packages/scanpy/_exporting.py in <listcomp>(.0)
301 out = []
302 for name,score in ctracks.items():
--> 303 line = name + ',' + ','.join(['%.3f' %x for x in score])
304 out += [line]
305 out = sorted(out,key=lambda x: x.split(',')[0])
TypeError: must be real number, not numpy.str_
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in scanpy/_exporting.py, focusing on spring_project and write_color_tracks at the failing line. Reproduce the export with the linked seurat2spring notebook and loom file, then inspect which color-track values reach the formatter. Done means the Seurat-to-scanpy-to-SPRING export completes without the reported TypeError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- bioinformatics, data-visualization
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100