syntenyPlotByR<br>

plot synteny genome alignment by mapper Mummer or LastZ using syntenyPlot.R.<br> plot assemblies comparison using comparePlot.R <br> <br> ###########<br> requriement<br> ###########<br> R 3.3+<br> optparse # an R package <br> <br> ###########<br> plot mummer delta file<br> ###########<br> There is a sample delta file and an output named "out.png" in project. user could try this by yourself.<br> <i>Rscript syntenyPlot.R -i <delta.file> -o out.png</i><br> <br> ###########<br> Large delta file<br> ###########<br> 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.<br> <i>perl nucmer2RPlotFormat.pl <delta.file> >out.format</i><br> <i>Rscript syntenyPlot.R -i <delta.file> -c -o out.png</i><br> <b>If the delta is formatted, the parameter -c should be setted.</b><br> <br> ###########<br> LastZ<br> ###########<br> There are two steps to format LastZ into our plot format. Only support one chromosome in Reference right now.<br> <i>perl maf2R_01.pl *.maf >out.maf_1</i><br> <i>perl maf2R_02.pl *out.maf_1 >out.maf_2</i><br> <i>Rscript syntenyPlot.R -i <out.maf_2> -c -o out.png</i><br> <b>If the delta is formatted, the parameter -c should be setted.</b><br>

###########<br> R Plot Format <br> ###########<br> 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.<br>

<p> refid # 1st columns <br> qryid # 2nd columns <br> reflen # 3rd columns <br> qrylen # 4th columns<br> refstart # 5th columns<br> refend # 6th columns<br> qrystart # 7th columns<br> qryend # 8th columns<br> refollen # 9th columns<br> belong ref start # 10th columns<br> belong ref # 11th columns<br> </p>

###########<br> Plot assemblies comparison <br> ###########<br> There is a sample of three alignment files using minimap and an output named "AssemblyCompare.png" in project. user could try this by yourself.<br> <i>Rscript comparePlot.R -i <alignment.files> -o out.png</i><br> <br> <br><br>