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cole-trapnell-lab / garnett

Automated cell type classification
MIT License
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Error in adjacent_vertices(x, i, mode = if (directed) "out" else "all") #50

Closed EleonoraLusito closed 3 years ago

EleonoraLusito commented 3 years ago

Hi, while doing the tutorial with pbmc data at https://cole-trapnell-lab.github.io/garnett/docs_m3/ during the classification (with/without markers) after doing str(pbmc_classifier) I found this Error (last lines):

Formal class 'garnett_classifier' [package "garnett"] with 4 slots ..@ classification_tree:List of 10 .. ..$ :List of 1 .. .. ..$ root: 'igraph.vs' Named int [1:2] 2 3 .. .. .. ..- attr(, "names")= chr [1:2] "B cells" "T cells" .. .. .. ..- attr(, "env")= .. .. .. ..- attr(, "graph")= chr "d739d599-3f8b-45e9-a0b5-6852523798d1" .. ..$ :List of 1 .. .. ..$ B cells: 'igraph.vs' Named int(0) .. .. .. ..- attr(, "names")= chr(0) .. .. .. ..- attr(, "env")= .. .. .. ..- attr(, "graph")= chr "d739d599-3f8b-45e9-a0b5-6852523798d1" .. ..$ :List of 1 .. .. ..$ T cells: 'igraph.vs' Named int [1:2] 4 5 .. .. .. ..- attr(, "names")= chr [1:2] "CD4 T cells" "CD8 T cells" .. .. .. ..- attr(, "env")= .. .. .. ..- attr(, "graph")= chr "d739d599-3f8b-45e9-a0b5-6852523798d1" .. ..$ :List of 1 .. .. ..$ CD4 T cells: 'igraph.vs' Named int(0) .. .. .. ..- attr(, "names")= chr(0) .. .. .. ..- attr(, "env")= .. .. .. ..- attr(, "graph")= chr "d739d599-3f8b-45e9-a0b5-6852523798d1" .. ..$ :List of 1 .. .. ..$ CD8 T cells: 'igraph.vs' Named int(0) .. .. .. ..- attr(, "names")= chr(0) .. .. .. ..- attr(, "env")= .. .. .. ..- attr(*, "graph")= chr "d739d599-3f8b-45e9-a0b5-6852523798d1" .. ..$ :Error in adjacent_vertices(x, i, mode = if (directed) "out" else "all") : At iterators.c:759 : Cannot create iterator, invalid vertex id, Invalid vertex id

Do you know something more about this bug and if/how it is possible to solve it?

Thank you in advance

hpliner commented 3 years ago

Hello, Is this just an issue with the str function? Do you run into problems while continuing the tutorial?

hpliner commented 3 years ago

I'm going to close, if this is still an issue, please reopen