Output matrix formatted wrong for tsv

kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

https://kharchenkolab.github.io/Baysor/

MIT License

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Output matrix formatted wrong for tsv #125

Closed Hannah-Doerpholz closed 3 weeks ago

Hannah-Doerpholz commented 3 months ago

I just ran Baysor v6.2.0 wit the flag --count-matrix-format tsv. In my output however, the genes are listed as the columns, but the matrix columns exceed the number of gene names. The rows however match the number of gene names. I think either the matrix needs to be transposed or the gene names need to be put as rownames, not column names. The cell names are also missing, so I can't really connect the information from the geojson polygons to the count matrix.

VPetukhov commented 2 months ago

Thank you for reporting it! That's definitely a bug.

VPetukhov commented 3 weeks ago

This is fixed in v0.7.0. Please, see the changelog for more details.