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JinmiaoChenLab / cytofkit2

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Cannot generate UMAP, TSNE works #34

Open HoxB8 opened 3 years ago

HoxB8 commented 3 years ago

Hello, I was able to run clustering on Rphenograph and generate TSNE maps. However, when I try to run UMAP, it throws the following error. Would you have an idea on how to troubleshoot this? Thank you.

Warning: Error in data.frame: arguments imply differing number of rows: 128000, 0 175: stop 174: data.frame 173: scatterPlot [./global.R#24] 169: C_ScatterPlotInput [C:\Program Files\R\R-4.1.0\library\cytofkit2\shiny/server.R#832] 168: renderPlot [C:\Program Files\R\R-4.1.0\library\cytofkit2\shiny/server.R#875] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$C_ScatterPlot 2: shiny::runApp 1: cytofkit_shiny_dashboard

raman91 commented 3 years ago

Please check if it works now. Thanks

HoxB8 commented 3 years ago

Hi raman91, I tried to re-install CyTOFkit2 and run the UMAP, but I still get the same error. I appreciate you looking into it.

raman91 commented 3 years ago

Thanks @HoxB8. Can you please try with the example fcs file located at inst/extdata/S4_PBMC.fcs and let us know if you can generate UMAP. You can also pass your log file to us.

HozaifaMetwally commented 3 years ago

Hi Raman91, I am Hozaifa, and I am new to R and Cytofkit. I am trying to do Cytof analysis using the Cytofkit and shiny app dashboard. I used the example fcs file located at inst/extdata/S4_PBMC.fcs. I could do data analysis, but when trying to use the data visualization using the shiny app (using the generated R file from the analysis) I cannot see anything, and I get errors of not finding scatterplot and heatmap functions. I attached screenshots here.

Thanks!

cytofkit_shiny dashboard cytofkit_shiny dashboard 2 shiny app

raman91 commented 3 years ago

Thanks @HozaifaMetwally. This was caused due to a change we made yesterday. Please try again now and let us know if you are able to run? Sorry for the inconvenience.

HozaifaMetwally commented 3 years ago

Hi Raman91, thanks for the prompt reply. Unfortunately, same error message still there. I will try again tomorrow and let you know. Thanks!

raman91 commented 3 years ago

Sure. You will have to install the cytofkit2 package again. Pls install again and check. Thanks

HozaifaMetwally commented 3 years ago

Thanks, Raman91! it is working now.