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normalize_by_total() fails after filter_cells() (update self.initial_cell_size) #37

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bobermayer opened this Issue Jan 12, 2018 · 1 comment

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bobermayer commented Jan 12, 2018

when filtering cells using vlm.filter_cells(totals > 500), only vlm.S and vlm.U get updated (resized), but vlm.initial_cell_size and vlm.initial_Ucell_size keep their original shapes. this leads to a

ValueError: operands could not be broadcast together with shapes (ncells_before,) (ngenes, ncells_after)

when calling vlm.normalize_by_total()

using vlm.initial_cell_size=vlm.initial_cell_size[(totals > 500)] fixes this problem

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gioelelm Jan 12, 2018

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Thank you for reporting! This is fixed in the new version 0.12.2, that I released just now. You don't need anymore the temporary fix vlm.initial_cell_size=vlm.initial_cell_size[(totals > 500)].

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gioelelm commented Jan 12, 2018

Thank you for reporting! This is fixed in the new version 0.12.2, that I released just now. You don't need anymore the temporary fix vlm.initial_cell_size=vlm.initial_cell_size[(totals > 500)].

@gioelelm gioelelm closed this Jan 12, 2018

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