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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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Problem of Clustering #207

Open biostat0903 opened 2 years ago

biostat0903 commented 2 years ago

Hi Ruben, When I use the example code of Giotto, I met a problem. Here is my code and error:

mini_visium <- doLeidenCluster(gobject = mini_visium, resolution = 0.4, n_iterations = 1000)
Error in bmerge(i, x, leftcols, rightcols, roll, rollends, nomatch, mult,  : 
  x.cell_ID is type environment which is not supported by data.table join

Please tell me how to solve the problem. Thanks!

Best, Sheng

RubD commented 2 years ago

Hi Sheng,

I can not reproduce your error running the code provided here: https://rubd.github.io/Giotto_site/articles/mini_visium.html

Did you ran this code in a new script, without loading anything prior to Giotto?

You could also try to reinstall the Giotto environment using installGiottoEnvironment(force_environment = T). This might fix the issue if it's related to python modules incompatibilities.

Let me know if this worked! Thanks, Ruben