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alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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antibody forests for sparse data #28

Closed EdGreen21 closed 1 year ago

EdGreen21 commented 1 year ago

I got Platypus using the devtools::install_github() command, and wanted to run Antibody forests on a sparse dataset from a autoimmune patient CSF sample:

AntibodyForests(VGM[[1]],
+                 network.algorithm = 'tree',
+                 specific.networks = 'clonotype1') %>% AntibodyForests_plot(node.label = NULL, node.scale.factor = 8)

And received the error:

Error in network.list[[i]] : subscript out of bounds

In all liklihood this means that there were too few B cells (275) to make a network, but I thought I'd flag this here with the suggestion of the function failing more informatively

tudorcotet commented 1 year ago

Hi! Thank you for your feedback - the AntibodyForests functions are still under development and we are glad to receive advice on how to improve the,. We plan to include some more intuitive error messages in the next CRAN push!