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sunduanchen / Scissor

Scissor package
GNU General Public License v3.0
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Some ideas about use our own seurat object #26

Closed GuohuaZhu closed 2 years ago

GuohuaZhu commented 2 years ago

Thanks for your wonderful packages. However, it seems unable to used at an integerated seurat object. After read the presubmited issues, I had know that the key parameters were 'data' and ‘RNA_snn”； So，Could I change the "CCA_snn" (aquired by an integrated Seurat object) into 'RNA_snn' and use the RNA assy aquire 'data' slot? Wishs for your reply. Thanks！

sunduanchen commented 2 years ago

I think so. You can have a try.

Thanks, Duanchen

GuohuaZhu commented 2 years ago

Thanks for your reply. I had try it and finaly get a result at my local R studio, while it failed on my remote R studio sever

jiexiong22 commented 2 years ago

Hello！Thank you for your excellent idea, and I tried your idea in local R studio, but still reported a same error. Could you please share the code you changed? Looking forward to your reply. Thanks!

GuohuaZhu commented 2 years ago

Hello！Thank you for your excellent idea, and I tried your idea in local R studio, but still reported a same error. Could you please share the code you changed? Looking forward to your reply. Thanks!

If you had look through the source code of the Scissor function, you would find that the main input this function needs is the RNA data of the Seurat object and its graph@RNA_snn object： sc_exprs <- as.matrix(sc_dataset@assays$RNA@data) network <- as.matrix(sc_dataset@graphs$RNA_snn) So，as the Seurat object RNA assay containing data，then we just need to assign 'CCA_snn' inside the integration object to 'RNA_snn' sc_dataset@graphs$RNA_snn <- sc_dataset@graphs$integrated_snn Then you can run the function.

jiexiong22 commented 2 years ago

Hello！Thank you for your excellent idea, and I tried your idea in local R studio, but still reported a same error. Could you please share the code you changed? Looking forward to your reply. Thanks!

If you had look through the source code of the Scissor function, you would find that the main input this function needs is the RNA data of the Seurat object and its graph@RNA_snn object： sc_exprs <- as.matrix(sc_dataset@assays$RNA@data) network <- as.matrix(sc_dataset@graphs$RNA_snn) So，as the Seurat object RNA assay containing data，then we just need to assign 'CCA_snn' inside the integration object to 'RNA_snn' sc_dataset@graphs$RNA_snn <- sc_dataset@graphs$integrated_snn Then you can run the function.

Thank you for your reply！ Your suggestions helped me solve the problem.