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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
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Some of the plots generated seems a bit weird... #279

Closed adhamzul closed 2 years ago

adhamzul commented 2 years ago

For the first time in a while, I wanted to do some tests on some of my earlier sequences. I installed NanoPlot through conda, and I also made sure it was up-to-date.

When I run the following code,

NanoPlot -o nanoplot_raw --readtype 1D --fastq 20210308_barcode06.fastq.gz --loglength -t 8

and I check the plots generated, some of the plots generated looked odd. And it is only visually, as the data points are accurate. Especially the KDE scatter plot.

It is not a massively urgent issue, but it seems to be bugging some people, and I totally get it...

I'm attaching the log file, and the plots produced.

Thank you very much for the great work!

Sincerely, Adham

LengthvsQualityScatterPlot_dot LengthvsQualityScatterPlot_kde LengthvsQualityScatterPlot_loglength_dot LengthvsQualityScatterPlot_loglength_kde Non_weightedLogTransformed_HistogramReadlength WeightedHistogramReadlength Yield_By_Length NanoPlot_20211110_1638.log

wdecoster commented 2 years ago

Can you elaborate on "the plots generated looked odd"? What did you expect to see instead? The KDE plots are indeed weirdly stretched horizontally, not sure on how to fix that, but what is wrong with the histogram of read lengths and the yield by length plot?

adhamzul commented 2 years ago

Hello Wouter,

Thank you for the response. It's mainly about how the KDE plots are stretched horizontally, but also on the point that both histograms of read lengths only have a vertical grid line.

Sorry for the unclear wording.

Regards, Adham

wdecoster commented 2 years ago

Personally I am not so bothered by only having vertical grid lines (happy to get more opinions though), but yes those KDE plots don't look nice at all. I have changed some code, and they should be more squared in v1.38.2, which will soon be available through the usual channels.

adhamzul commented 2 years ago

Good morning Wouter,

I cannot express how grateful I am! Thank you very much for the responses!

Will update NanoPlot soon.

Best wishes, Adham