orthodotter -h
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orthodotter - Plot orthologous genes on an oxford grid.
-f <file> : input file, containing orthologous genes, default is stdin
species chr-name start end species chr-name start end
-toPlot <arg> : give the x and y sets and the color separated by double-dots,
for example set1:set2:red will plot set1 on x, set2 on y with
red points. Could give several -toPlot arguments.
To launch the clustering of dots, use extra-option 1=dist,min_nb_genes
where dist is the minimal distance (euclidian) between two points and min_nb_genes the minimal
number of genes in a cluster to be valid.
-o <file> : output file, default is stdout
-x <int> : resolution of x axis, default is 600
-y <int> : resolution on y axis, default is 600
-r <int> : radius of circle representing orthologous genes
-format : could be png, gif, jpg, pdf or ps. Default is png.
-fg : foreground color, default is black
-bg : background color, default is transparent
-fSize <int> : fontSize, default is 1
-filter : check chromosome names
-h : help
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orthodotter -f Vigne_Banane.ortho -toPlot Vigne:Banane:black:1=10,5 -x 1200 -y 1200 -bg white -o Vigne_vs_Banane.png > Vigne_vs_Banane.clusters
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