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navinlabcode / copykat

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extracting subclone info after running heatmap.3 #32

Closed ckb19 closed 2 years ago

ckb19 commented 3 years ago

Hi,

Thanks for the great tool! I'm having some trouble navigating my way around the copykat object.

I've generated informative tumour v normal and tumour subclone heatmaps for my dataset, but can't figure out where the subclone info linked back to the cell barcode is stored. This would be useful to allow integration with the scRNA-seq workflow, e.g. to project onto UMAP and integrate with gene expression data. Is this easily accessible within the object?

Grateful for any advice/code. Thanks!

yuGithuuub commented 3 years ago

The annotation information can be obtained from the prediction slot

pred.test <- data.frame(copykat.test$prediction)

Prakrithi-P commented 1 year ago

The annotation information can be obtained from the prediction slot

pred.test <- data.frame(copykat.test$prediction)

Hi, This tells only if the cell is aneuploid or diploid but nothing about the subclones. Is there a way to group the barcodes based on subclones as we could see from the branches of the dendrogram from the Heatmap?

Thanks!