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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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runVIZ for 3D plotting #87

Closed yasserIRCM closed 5 years ago

yasserIRCM commented 5 years ago

Hi

I would like to have three UMAP embeddings per cell to have a 3D plot. so I installed umap-learn using install.packages("reticulate") library(reticulate) reticulate::py_install(packages ='umap-learn')

yet runViz is rejecting the command and reporting the following message Error in runViz1(obj = x.sp, tmp.folder = tempdir(), dims = 3, eigs.dims = c(1:26), : Please install umap - learn more at https://cran.r-project.org/web/packages/umap/index.html

could you please let me know how to modify the runviz source so I can 3 UMAP embeddings?

thanks a lot.

r3fang commented 5 years ago

Hi, maybe try this: umap.cor =umap(x.sp@smat@dmat[,1:26])

Unfortunately, snapATAC does not support visualizing 3D plot.

Best,

yasserIRCM commented 5 years ago

ok, I will try it and let you know

yasserIRCM commented 5 years ago

Hi there I used this umap.cor =umap(x.sp@smat@dmat[,1:26], method="umap-learn", n_components=3)

and it worked thanks a lot I am closing the issue