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Problem with generating JaBbA plots #32
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Assuming the |
I get this:
Also, there is the first error too. I shouldn't have to run it twice to pass that error. Thank you! |
The first error is related to the second (the referenced code is from gTrack, which is used to plot the gGraph). There is a function that validates gTrack inputs which is failing on the In the meantime, since the output files are being generated you should still be able to explore them. (See the relevant section in the JaBbA readme here, if you haven't already: https://github.com/mskilab-org/JaBbA#output) |
Thank you, that worked to install JaBbA with Gurobi! However, I am now trying to run it on the simple example provided and I'm running into some problems.
jba ${JABBA_PATH}/junctions.vcf ${JABBA_PATH}/coverage.txt --gurobi TRUE
, it doesn't find the segmentation, so it runs segmentation, it saves the seg.rds file, but then it gives an error:" .....
JaBbA 2023-10-16 16:29:56.631185: No segmentation provided, so performing segmentation using CBS
JaBbA 2023-10-16 16:29:56.694123: Segmentation finished
.....
JaBbA 2023-10-16 16:29:58.848608: Built gGraph with 82 nodes, 104 edges, purity 0.6, and ploidy 1.93
Error in !is.null(formatting(object)$y.field) && !is.na(formatting(object)$y.field) :
'length = 2' in coercion to 'logical(1)'
Calls: suppressPackageStartupMessages ... validObject -> anyStrings -> isTRUE -> validityMethod
"
" ...
Generating figures
JaBbA 2023-10-16 16:46:15.355457: Something wrong with plotting JaBbA results. Please try it later.
JaBbA 2023-10-16 16:46:15.382705: Something wrong with plotting JaBbA simplified results. Please try it later.
..."
Thank you for your help!
Originally posted by @mandronescu in mskilab-org/JaBbA#94 (comment)
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