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`set_clusters` should use string type for cluster labels for hdf5 dump #40

bobermayer opened this Issue Jan 18, 2018 · 2 comments


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bobermayer commented Jan 18, 2018

when setting clusters from an external data frame (eg., read Seurat output using pandas with vlm.set_clusters(my_annotation.loc[['CellID'],'cell.type'])), the dtype of vlm.cluster_labels is 'O', which cannot be dumped into hdf5 (TypeError: Object dtype dtype('O') has no native HDF5 equivalent).
using vlm.cluster_labels=vlm.cluster_labels.astype(np.string_) fixes this problem but creates byte strings which is maybe not optimal. some unicode compatibility problem?

great package by the way!

@gioelelm gioelelm closed this in d450968 Jan 18, 2018


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gioelelm commented Jan 18, 2018

Thank for reporting the bug, it was a little rare use case, but I fixed anyways in v0.12.4

great package by the way!

Thank you!


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yueqiw commented Jun 23, 2018


I'm running into the same issue with vlm.set_clusters() using Scanpy output. The dtype of vlm.cluster_labels and vlm.colorandum (Hex color code) are '<U2' and '<U7', and this causes error in vlm.to_hdf5().

The following code fixes the problem:

if x.dtype.kind == 'U': x = x.astype(np.string_)
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