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hewm2008 / NGenomeSyn

Any Way to Show Multi genomic Synteny
MIT License
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How do I change the colors of ribbons? #4

Open kushalsuryamohan opened 1 year ago

kushalsuryamohan commented 1 year ago

Hi, I am trying to plot synteny between 5 genomes. I have calculated pairwise synteny blocks as follows: Ref genome <-> species 1 species 1 <-> species 2 species 2 <-> species 3 species 3 <-> species 4

I want to show a synteny plot of all 5 genomes to look at the evolution of chromosomes from an ancestral species (ref genome) to the most recently evolved species (species 4). How do I customize the colors of the ribbons so that each chromosome/scaffold gets a color of my choice?

Thank you!

hewm2008 commented 1 year ago

LinkFileRef1VsRef2 format:

chrB1 1 1000000 LG01 100000 1 
chrB3 1 1000000 LG02 1 1000000 fill=”#F8F8F8”  stroke=”#F8F8F8”
chrB2 100 1 LG03 500 8000  fill=red  stroke=red    stroke-opacity=0.5   fill-opacity=0.5

we define the suffix name of these files as xx.link , like RefA_vs_RefB.link RefC_vs_RefB.link… the fill and stroke You can configure different color properties of different chr in the link file ( fill and stroke). For more specific configurations, see example and user manual