Lyla Atta

icon indicating a website link https://lylaatta.github.io/

icon company Johns Hopkins University icon location Baltimore, MD icon location MD-PhD Candidate in the Department of Biomedical Engineering at Johns Hopkins University.

Results 7 comments of Lyla Atta

Error in scv$pl$velocity_embedding_stream

Hi, Thanks for trying out the package! Can you please provide the part of the code that generated the error? Thanks!

Error in layout_with_fr(g, dim = 2) : At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value

Hi Eunha, Thank you for trying out the package and for your question. Could you please provide a reproducible example for the issues you're having? For 2., a common issue...

Error in layout_with_fr(g, dim = 2) : At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value

Hi Eunha, From the error you included, it seems like your graph has edge weights that are non-positive. Without the specific data that you're working with, it's difficult for me...

Error in layout_with_fr(g, dim = 2) : At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value

Great! Out of curiosity, what was the source of the error? For veloviz embedding parameters, optimal parameter choices are data dependent but I generally find that the default parameters are...

Error in layout_with_fr(g, dim = 2) : At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value

I usually start with a k=0.1*N where N is the number of cells in your dataset and distance.weight=1 and explore variations on parameter values from there. There isn't really a...

Error in layout_with_fr(g, dim = 2) : At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value

Hi @galaxyeee , I was able to reproduce your initial error: `Error in layout_with_fr(g, dim = 2) : At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value`...

Error in layout_with_fr(g, dim = 2) : At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value

Hi @parkjooyoung99, I'm not sure what the latest igraph version that works is but igraph 1.2.6 works for me. Alternatively, I have updated the package to work with the latest...