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hylasD / tSpace

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Integration tSpace and seurat object #4

Open dianadom opened 4 years ago

dianadom commented 4 years ago

Hi,

Do you know how to upload data from seurat object to tSpace and also save the same plot (based in UMAP embeddings from seurat)?

hylasD commented 4 years ago

Hi

The easiest way is to export desired number of principal components from Seurat object and use them as a data for tSpace analysis.

Another option is to export scaled gene expression values of the variable genes from Seurat and use them for tSpace analysis. Due to larger number of genes calculation will be slower.

I am not sure what you mean with saving the umap plot. In any case I suggest to explore Seurat package tutorials and how to web pages for all the questions regarding Seurat. The structure of Seurat object is quite complex (S4 type object) however principal components and scaled data are just R dataframes buried into slots of S4 Seurat object.

Here is what I was able to find online

https://github.com/satijalab/seurat/issues/1902

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On Oct 9, 2020, at 11:52 AM, dianadom notifications@github.com wrote:

 Hi,

Do you know how to upload data from seurat object to tSpace and also save the same plot (based in UMAP embeddings from seurat)?

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