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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
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Weigted Histogram #350

Open AsmaaSamyMohamedMahmoud opened 9 months ago

AsmaaSamyMohamedMahmoud commented 9 months ago

Hi, I'm using NanoPlot v1.42 and noticed that the y-axis title of the weighted histogram (normal and log transformed) is number of bases not number of reads as non-weighted histogram. can you please clarify it and also explain to me how the histogram is weighted ? I just have another comment if you can consider it, green color of histograms is so light, especially the generated figures in the directory. When I downloaded from the html report, color was more visible but it's png while I wanted to get the figures in svg format. I attached an example for your review. fig1 fig1_htmlreport

Thank you, Asmaa

wdecoster commented 9 months ago

See also https://github.com/wdecoster/NanoPlot/issues/111

And there is a --color argument to change the color. Does that help?

AsmaaSamyMohamedMahmoud commented 9 months ago

Thank you, I got how it is weighted from https://github.com/wdecoster/NanoPlot/issues/111 but it is not clear for me how max of y-axis of non-weighted hist after log transformation is 80k reads while max of y-axis of weighted hist after log transformation is 60k bases. WeightedLogTransformed_HistogramReadlength Non_weightedLogTransformed_HistogramReadlength

AsmaaSamyMohamedMahmoud commented 9 months ago

I tired the blue color and it is much better. Thank you.

AsmaaSamyMohamedMahmoud commented 9 months ago

Hi wdecoster, Do you have any idea why I got this output with the log transformed plots ? Based on https://github.com/wdecoster/NanoPlot/issues/111, the issue of y-axis was supposed to be fixed in v1.26 and I'm using v1.42.

Thank you,