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markrobinsonuzh / cytofWorkflow

MIT License
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Error in Isomap using plotDR #26

Closed LeleDR closed 3 years ago

LeleDR commented 3 years ago

Hi!

I am pretty new here so let me know I need to put more information in my message. I have been using the CytofWorkFlow package for a few days now and this morning I was able to produce the UMAP with my data but since noon I got an error message while using the same data and the same script :

plotDR(sce, "UMAP", color_by = "CD4")

Error in Isomap(data, 2, min(10, data_points - 1)) : invalid argument: data argument is required to be a N x D matrix (N samples, D features) De plus : Warning message: In plotDR(sce, "UMAP", color_by = "CD4") : dimension of given data is too high (172791); used Isomap to reduce it to 2 dimensions

I got no error before this all the figure were generated normally .

I am able to generate the heatmap using :

plotMultiHeatmap(sce, hm1 = "type", hm2 = "pS6", k = "meta20", row_anno = FALSE, bars = TRUE, perc = TRUE)

I got no error message running

sce <- runDR(sce, "UMAP", cells = 1e3, features = "type")

I also tried back with the example data and I get the same error now while I was able to generate all the figures with it at the beginning of the week.

Can it be some kind of internal problem with a package? Should I wait?

Thank you a lot

Best

Lea

HelenaLC commented 3 years ago

duplicate of https://github.com/HelenaLC/CATALYST/issues/206