Write fcs function
mbuttner opened this issue · comments
Maren Büttner commented
Pytometry should include a function to export an anndata file to fcs
using the Gating ML 2.0 version and FCS standard 3.*
Quentin Blampey commented
Gregor Sturm commented
A couple points from the discussion in scverse/governance#64:
- There was some agreement that it makes sense to keep IO separate from the rest in readfcs. I'm sure they would be happy to include functions for writing FCS filese
- Here it could make sense to either switch to @whitews's FlowIO package or use it as another backend in
readfcs
.
adata = readfcs.read("sample.fcs", backend="fcsparser")
adata = readfcs.read("sample.fcs", backend="flowio")
readfcs.write(adata, "sample.fcs", backend="flowio")
- Or maybe to add support for AnnData directly in FlowIO?
pip install flowio[anndata]
adata = flowio.FlowData('sample.fcs').to_anndata()