Comments (10)
The visualization is not made for 1000 haplotypes. I suggest you use your own--a simple line plot will do just fine! In fact, also panacus
is not yet optimized for such a pangenome size, but an implementation is underway...
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I went for R, that's why I am asking
I see you are using a Seaborn color palette. I will get it going somehow!
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There you go... const PCOLORS = ['#f77189', '#bb9832', '#50b131', '#36ada4', '#3ba3ec', '#e866f4'];
-> https://github.com/marschall-lab/panacus/blob/f2a1ca8278ac4e087acfec5ea471aff072b1fa34/etc/lib.js#L5C1-L5C84
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Do you have the HEX of all these colors somewhere for me? So I can at least make it look like it came from panacus ;)
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I suggest the following: Take the panacus-visualize
script, dump it in a Jupyter Notebook, re-use the functions, and change those that you want to improve on. The script is simple and easy to understand. That's at least what I am doing if I need to customize panacus output. At some point, I should provide such a notebook in the repository.
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Alright, now panacus itself seems to be overwhelmed:
RUST_LOG=info panacus histgrowth ecoli2146.pan.explode.0.og.crush.gfa -c bp -q 0,1,0.5,0.1 -t 28 > ecoli2146.pan.explode.0.og.crush.gfa.histgrowth.tsv
This results in a huge number of NaN
in the resulting TSV. Any ideas?
ecoli2146.pan.explode.0.og.crush.gfa.histgrowth.txt
The lengths of the paths vary a lot, maybe this is the problem?
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I'm surprised that this doesn't work, and I suspect it's a fixable bug. @lucaparmigiani what do you think?
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Thanks Simon for letting us know about the NaN!
It was indeed a bug and your graph was causing a f64 overflow!!
Now the values are handled better and it is fixed. You can run it on your graph :)
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Thanks @lucaparmigiani
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Indeed this solved the issue, thanks!
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Related Issues (20)
- Option to output plots in separate PNG files HOT 11
- Could you please make an new release? HOT 3
- command is not supported for more than 65534 HOT 6
- How to Visualize the results of the minigraph-cactus? HOT 21
- Request software updates HOT 6
- Feature request: Alternative plot with #nodes/#edges vs AC
- A problem while running panacus-visualize HOT 1
- Update Readme to reflect installation of python dependencies in the installation section. HOT 1
- compiler error in rustc-serialize HOT 3
- Haplotype labels in TSV, visualisations ? HOT 8
- how is panacus treating Ns HOT 4
- Discrepancy between graph length, reference length, and novel base pairs HOT 3
- macOS binary missing HOT 1
- Calling `panacus hist` with `-s` but then not supplying the subset file cases no error
- coverage/quorum HOT 1
- what dose coverage and quorum mean๏ผ HOT 3
- Merge different chroms stats into one graph HOT 3
- path coordinates HOT 8
- After `panacus hist` and `panacus growth`, the final visualization will show `#nodes` instead of `bps`. I use `-c bp` for hist HOT 1
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