https://github.com/shingocat/syntenyPlotByR

plot genome alignment synteny
https://github.com/shingocat/syntenyPlotByR

Last synced: 4 months ago
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plot genome alignment synteny

• Host: GitHub
• URL: https://github.com/shingocat/syntenyPlotByR
• Owner: shingocat
• License: gpl-3.0
• Created: 2018-04-10T03:48:57.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2020-05-25T07:59:28.000Z (about 4 years ago)
• Last Synced: 2024-03-16T06:35:38.977Z (4 months ago)
• Language: R
• Size: 319 KB
• Stars: 18
• Watchers: 2
• Forks: 7
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• repo-5916-awesome-genome-visualization - syntenyPlotByR - genome-visualization/synteny_plot_by_r.png) (Dotplot)
• awesome-genome-visualization - syntenyPlotByR

README

        
# syntenyPlotByR


plot synteny genome alignment by mapper Mummer or LastZ using syntenyPlot.R.


plot assemblies comparison using comparePlot.R 





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requriement


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R 3.3+


optparse # an R package 





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plot mummer delta file


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There is a sample delta file and an output named "out.png" in project. user could try this by yourself.
 

Rscript syntenyPlot.R -i  -o out.png





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Large delta file


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If the delta file is too large, it is very time-consuming for ploting it. We recommand format the delta file by our PERL script firstly. And then plot the format delta file.


perl nucmer2RPlotFormat.pl  >out.format


Rscript syntenyPlot.R -i  -c -o out.png


If the delta is formatted, the parameter -c should be setted.





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LastZ


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There are two steps to format LastZ into our plot format. Only support one chromosome in Reference right now.


perl maf2R_01.pl *.maf >out.maf_1


perl maf2R_02.pl *out.maf_1 >out.maf_2


Rscript syntenyPlot.R -i  -c -o out.png


If the delta is formatted, the parameter -c should be setted.


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R Plot Format 


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There are 11 columns in Our R plot Format. User could change any alignment format into our R plot format and then plot it by our R script. And there is a sample file named "out.format" in project.




refid # 1st columns 


qryid # 2nd columns 


reflen # 3rd columns 


qrylen # 4th columns


refstart # 5th columns


refend # 6th columns


qrystart # 7th columns


qryend # 8th columns


refollen # 9th columns


belong ref start # 10th columns


belong ref # 11th columns




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Plot assemblies comparison 


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There is a sample of three alignment files using minimap and an output named "AssemblyCompare.png" in project. user could try this by yourself.
 

Rscript comparePlot.R -i  -o out.png