Velocity analysis

[jphe]

Hi,

When I run Velocity analysis with the pancreas_sub data,

pancreas_sub <- RunSCVELO(
  srt = pancreas_sub, group_by = "SubCellType",
  linear_reduction = "PCA", nonlinear_reduction = "UMAP"
)
VelocityPlot(srt = pancreas_sub, reduction = "UMAP", group_by = "SubCellType")

It reports an error:

'misc' slot is not converted.

'tools' slot is not converted.

Error in py_call_impl(callable, dots$args, dots$keywords): NotImplementedError: Cannot 

Traceback:

1. RunSCVELO(srt = pancreas_sub, group_by = "SubCellType", linear_reduction = "PCA", 
 .     nonlinear_reduction = "UMAP")
2. do.call(SCP_analysis$SCVELO, args)
3. (structure(function (...) 
 . {
 .     dots <- py_resolve_dots(list(...))
 .     result <- py_call_impl(callable, dots$args, dots$keywords)
 .     if (convert) 
 .         result <- py_to_r(result)
 .     if (is.null(result)) 
 .         invisible(result)
 .     else result
 . }, class = c("python.builtin.function", "python.builtin.object"
 . ), py_object = <environment>))(adata = <environment>, h5ad = NULL, 
 .     group_by = "SubCellType", n_jobs = 1L, linear_reduction = "PCA", 
 .     nonlinear_reduction = "UMAP", basis = NULL, mode = "stochastic", 
 .     fitting_by = "stochastic", magic_impute = FALSE, knn = 5L, 
 .     t = 2L, min_shared_counts = 30L, n_pcs = 30L, n_neighbors = 30L, 
 .     approx = TRUE, stream_smooth = NULL, stream_density = 2L, 
 .     arrow_length = 5L, arrow_size = 5L, arrow_density = 0.5, 
 .     denoise = FALSE, denoise_topn = 3L, kinetics = FALSE, kinetics_topn = 100L, 
 .     calculate_velocity_genes = FALSE, show_plot = TRUE, dpi = 300L, 
 .     save = FALSE, dirpath = "./", fileprefix = "")
4. py_call_impl(callable, dots$args, dots$keywords)

[XiaolongYang-HZAU]

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