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KrishnaswamyLab / phemd

Identifying cell subpopulational differences among single-cell biospecimens
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Error message in embedCells #2

Closed mdmanurung closed 4 years ago

mdmanurung commented 4 years ago

Hi, I am trying to use the package for CyTOF data analysis. When I am running the plotEmbedding function, I got the following message:

Error in seq.int(0, 1, length.out = n) : 
  'length.out' must be a non-negative number
In addition: Warning message:
In max(state_labels) : no non-missing arguments to max; returning -Inf

What would be the cause of the problem?

wschen commented 4 years ago

Which method are you using to generate your cell-state embedding (Monocle2, PHATE, Seurat?) You would need to run the embedCells and, in the case of Monocle2, orderCellsMonocle functions before plotEmbedding.