Closed Bio-data-tricks closed 3 years ago
I would like to use some scanpy functions, especially the visualization of paga connections, or graph representation. However when I try to use umap in scanpy or in dynverse I don't get the same exact results. Are the parameters the same?
My code in dynverse:
model_paga <- infer_trajectory( dataset = dataset_with_prior, method = dynmethods::ti_projected_paga(filter_features = FALSE, n_neighbors =15L, resolution = 1.2L, embedding_type = "umap") plot_dimred(model_paga, grouping = group_onto_nearest_milestones(model_paga), label_milestones=TRUE)
Does anyone have an idea ?
Thank you
Nicolas
I would like to use some scanpy functions, especially the visualization of paga connections, or graph representation. However when I try to use umap in scanpy or in dynverse I don't get the same exact results. Are the parameters the same?
My code in dynverse:
model_paga <- infer_trajectory( dataset = dataset_with_prior, method = dynmethods::ti_projected_paga(filter_features = FALSE, n_neighbors =15L, resolution = 1.2L, embedding_type = "umap") plot_dimred(model_paga, grouping = group_onto_nearest_milestones(model_paga), label_milestones=TRUE)
Does anyone have an idea ?
Thank you
Nicolas