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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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No dimensionality reduction found. #187

Closed victorwang123 closed 1 year ago

victorwang123 commented 2 years ago

Thanks for your amazing tool! I got a part of clusters(0-4) from my seurat datasets. And it seems wrong. Can you help me? Here are my scripts:

ep_me<-subset(sce.me_ep_v1, idents = c(0,1,3,4)) ep.sce<-as.SingleCellExperiment(ep_me) sim <- slingshot(ep.sce,clusterLabels = 'cell_type')

it shows: Error in .local(data, clusterLabels, ...) : No dimensionality reduction found.

My datasets: An object of class Seurat 25184 features across 12251 samples within 2 assays Active assay: RNA (23184 features, 0 variable features) 1 other assay present: integrated 2 dimensional reductions calculated: pca, umap

Thanks

kstreet13 commented 2 years ago

Hi @victorwang123,

Thanks for the report! It looks like something is happening when you convert between Seurat and SCE that is causing the loss of the dimensionality reductions. Can you check that your SCE (ep.sce) has them?

Also, when there's more than one dimensionality reduction, I would recommend specifying which one slingshot should use (ie. setting reducedDim = 'pca', if you intend for it to use PCA).

Best, Kelly