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TrigosTeam / SPIAT

https://trigosteam.github.io/SPIAT/
Artistic License 2.0
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After deletion of mis-classified cells from the image, TSNE plot is not generating #10

Closed yuvibim08 closed 2 years ago

yuvibim08 commented 2 years ago

Please check for the issue

After running the following script given error is occurred : script:
cell_type_image1 <- select_celltypes(cell_type_image, c("Cell_3302", "Cell_4917", "Cell_2297", "Cell_488", "Cell_4362", "Cell_4801", "Cell_2220", "Cell_3431", "Cell_533", "Cell_4925", "Cell_4719", "Cell_469", "Cell_1929", "Cell_310", "Cell_2536", "Cell_321", "Cell_4195"), feature_colname = "rowname", keep = FALSE)

           g_1 <- dimensionality_reduction_plot(cell_type_image1, plot_type = "TSNE", 
                               feature_colname = "Cell.Type")

Error: Error in .check_tsne_params(nrow(X), dims = dims, perplexity = perplexity, : perplexity is too large for the number of samples TSNE_plot_error

fuerzhou commented 2 years ago

Hi @yuvibim08,

Thank you very much for raising the issue. Your contribution is important to the tool development.

I suspect that the issue is within our code. I will check our function and get back to you as soon as possible.

Thank you again for your contribution!

yuvibim08 commented 2 years ago

Thank you for your reply, I will contact you through the mail.

fuerzhou commented 2 years ago

The function has been updated in v0.99.2. Now dimensionality_reduction_plot() has a new parameter perplexity. perplexity is adjusted based on the number of samples (cells) in the image. It can also be manually specified.