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alexQiSong / scSTEM

Single cell STEM (scSTEM) is a shiny app based R package for visualizing and clustering genes in pseudotime ordered single cell RNA-seq data. scSTEM is a GUI based tool and thus does not require any coding experience.
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UI crashes with error "Error in [[<-: 0 elements in value to replace 103766 elements" #3

Open sciotlos opened 2 years ago

sciotlos commented 2 years ago

Hello,

I've tried scSTEM with both the sample data and my own data. After loading the data, I try to proceed to the UMAP step. However I get the following warnings and ultimately the GUI crashes. Here are the warning and error messages, when I try to run with the sample data:

Warning in monocle3::new_cell_data_set(expression_data = rv$counts, cell_metadata = rv$cell_meta, : gene_metadata must contain a column verbatim named 'gene_short_name' for certain functions.

Warning: Error in [[<-: 0 elements in value to replace 103766 elements 3: shiny::runApp 2: shiny::runGadget 1: run_scstem_GUI

So, it seems to make it past new_cell_data_set, except for the 'gene_short_name' warning. However I can't figure out where exactly it's crashing. Any idea why this is happening, even with the data included with the package?

Thank you!

alexQiSong commented 2 years ago

Hi Sciotlos,

Thank you for your interest in scSTEM! I'm sorry for getting back to you late. It is weird that I did not receive GitHub notification email for new issues. Were you able to solve your issue? It looks like you were running the sample data, right?

What is your OS? Usually the 'gene_short_name' warning wouldn't be a big issue.

Thanks, Qi

alexQiSong commented 2 years ago

Hello,

I've tried scSTEM with both the sample data and my own data. After loading the data, I try to proceed to the UMAP step. However I get the following warnings and ultimately the GUI crashes. Here are the warning and error messages, when I try to run with the sample data:

Warning in monocle3::new_cell_data_set(expression_data = rv$counts, cell_metadata = rv$cell_meta, : gene_metadata must contain a column verbatim named 'gene_short_name' for certain functions.

Warning: Error in [[<-: 0 elements in value to replace 103766 elements 3: shiny::runApp 2: shiny::runGadget 1: run_scstem_GUI

So, it seems to make it past new_cell_data_set, except for the 'gene_short_name' warning. However I can't figure out where exactly it's crashing. Any idea why this is happening, even with the data included with the package?

Thank you!

I realized you might not get notified by my post above. Trying again here. Please let me know if you see my comment. 😀