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Published 20 hours ago • verified publisher icon velocyto-team

Velocyto on Monocle coordinates

Open andrea-de-micheli opened this issue 5 years ago • 8 comments

Hi, just wondering why show.velocity.on.embedding.cor() would fail on Monocle coordinates? Thank you, Andrea

andrea-de-micheli avatar Jul 18 '19 15:07 andrea-de-micheli

Hi @andrea-de-micheli, I had issues with the same function when importing SPRING coordinates. What I realized was the coordinates needed to be within the scale of at most 10-20. Turns out its mentioned in the documentation but I missed it. When dividing my coordinates by 100 or 1000 to bring within the -10 - 10 scale then everything worked fine.

mbassalbioinformatics avatar Jul 23 '19 21:07 mbassalbioinformatics

@andrea-de-micheli ,You may have set the wrong coordinates.

ZHANGHAO007 avatar Sep 21 '19 10:09 ZHANGHAO007

Thank you for your inputs @mbassalbioinformatics @ZHANGHAO007. I will try that!

andrea-de-micheli avatar Sep 24 '19 21:09 andrea-de-micheli

Hello again,

My monocle data ranges from about -10 to 10 in one dimension and -5 to 5 in the other. Yet I am getting this error while velocyto calculates the arrows. Any ideas where I should start to troubleshoot this?:

Thanks! :)

calculating arrows ... Error in embArrows(emb, tp, arrow.scale, n.cores) : 
  Not compatible with requested type: [type=list; target=double].

andrea-de-micheli avatar Oct 11 '19 17:10 andrea-de-micheli

Id just try going smaller still maybe even divide the coordinates by 10 and see how it goes. For me I just kept going smaller and smaller till it eventually worked. Hope that helps.

mbassalbioinformatics avatar Oct 12 '19 11:10 mbassalbioinformatics

Hello again,

My monocle data ranges from about -10 to 10 in one dimension and -5 to 5 in the other. Yet I am getting this error while velocyto calculates the arrows. Any ideas where I should start to troubleshoot this?:

Thanks! :)

calculating arrows ... Error in embArrows(emb, tp, arrow.scale, n.cores) : 
  Not compatible with requested type: [type=list; target=double].

Hello, have you solved this problem? I encountered the same issue

genereader avatar Nov 04 '19 08:11 genereader

Hello again,

My monocle data ranges from about -10 to 10 in one dimension and -5 to 5 in the other. Yet I am getting this error while velocyto calculates the arrows. Any ideas where I should start to troubleshoot this?:

Thanks! :)

calculating arrows ... Error in embArrows(emb, tp, arrow.scale, n.cores) : 
  Not compatible with requested type: [type=list; target=double].

Hi @andrea-de-micheli , you may have the "emb" input as a dataframe. Converting it to a matrix may help to solve the problem.

yingyonghui avatar Nov 29 '19 08:11 yingyonghui

Converting it to a matrix may help to solve the problem.

thanks, I had the same issue and this helped

eregenyi avatar May 05 '21 08:05 eregenyi