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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
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syntenic links have no color #46

Closed Zefeng-Wu closed 1 year ago

Zefeng-Wu commented 1 year ago

Hi, I am using plotsr to visualize the syri.out file using the default parameters and produced a pdf plot file. But I found the syntenic links have no color, and are not the defaulted gray color. Then I added a "--cfg base.cfg" option and modified the plot colors, it still did not work. plotsr --version 1.0.0

mnshgl0110 commented 1 year ago

Have you tried running the examples (https://github.com/schneebergerlab/plotsr/tree/master/example)? Are they working? I suspect that this is either caused by something in input or just how the plots are visualised on a monitor (try printing the plots). In the base.cfg file, try setting syncol to #000000 (black) and also try the -R parameter of plotsr. If none of this works then I would need a test dataset to reproduce this issue.

Zefeng-Wu commented 1 year ago

Thanks, it was indeed the PDF viewer that caused the problem, now it can show call the colors in the pdf pictures.