Problem with generating JaBbA plots

[shihabdider]

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.

1. The first time I run it with 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
"

2. Then, if I run it the second time, since it has the segmentation file it uses it, it seems to work fine, it creates the jaba.simple.gg.rds file, but then it gives some plotting errors:

" ...
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)

[shihabdider]

Assuming the jabba.rds file was generated, could you please load this file (e.g using loadRDS()) and return its$gtrack and $agtrack attributes?

[mandronescu]

I get this:

> jobj <- readRDS("jabba.rds")
> jobj$gtrack
gTrack object with 1 tracks with formatting:
  y.field  name draw.paths height ygap path.col path.lwd stack.gap col border angle draw.var
1      cn JaBbA      FALSE     10    2    black        1         0  NA     NA     0    FALSE
  gr.colorfield y.quantile cex.label gr.cex.label.gr gr.srt.label y.cap lwd.border hadj.label
1            NA       0.01         1             0.8            0  TRUE          1          1
  vadj.label smooth round ywid ypad circles lines  bars triangle ylab max.ranges
1        0.5     NA    NA   NA    0   FALSE FALSE FALSE    FALSE           50000
  source.file.chrsub y0.bar yaxis.pretty yaxis.cex chr.sub edgevars gr.labelfield grl.labelfield
1               TRUE     NA            5         1    TRUE       NA            NA             NA
  grl.colorfield NA. xaxis.prefix xaxis.unit xaxis.suffix xaxis.round xaxis.interval
1             NA  NA                       1                        3           auto
  xaxis.cex.label xaxis.newline xaxis.chronly xaxis.width labels.suppress labels.suppress.gr
1               1          TRUE         FALSE        TRUE           FALSE              FALSE
  labels.suppress.grl xaxis.label.angle xaxis.ticklen xaxis.cex.tick sep.lty sep.lwd sep.bg.col
1               FALSE                 0             1              1       2       1     gray95
  sep.draw y0 y1 m.sep.lwd cmap.min cmap.max bg.col yaxis
1     TRUE NA NA         1       NA       NA  white  TRUE
> jobj$agtrack
NULL

Also, there is the first error too. I shouldn't have to run it twice to pass that error. Thank you!

[shihabdider]

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 y.field parameter. Based on your output it seems like the y.field is correctly set to cn for $gtrack. Therefore, I suspect the error might be coming from $agtrack being NULL. I will look into this further and get back to you.

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)