markrobinsonuzh/cytofWorkflow

Error in Isomap using plotDR

LeleDR opened this issue · 1 comments

LeleDR commented

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