repeatviz.pl −− visualize a bunch of repeats using graphviz
repeatviz.pl <input> [output]
output is defined based on the input name unless otherwise specified
Options: −−echo shows all input to R (very spammy). −−colors={rainbow,heat,terrain,topo,cm,cool} uses an alternate color palette (default is rainbow). Custom palettes can also be created by providing a list of colors (like red,yellow,blue). −−colorby={size,id,density} specify what to select colors based on (default is id) −−density={N} sample repeat density at every N bp (default calculates a value based on width*res and genome size) −−coloropts={extra options to pass to R's color generator} −−connect draw connecting edges for points in adjacent sequences −−maxlines={N} don't draw lines to connect cluster−sequence pairs with more than N edges −−size={N} size of dots −−bigfirst plot big clusters first −−smallfirst plot small clusters first(default) −−res={DPI} defaults to 96 −−width|height={N} graph size in inches −−legend={position} position to place legend (R keywords like "right" or "topright" are good) −−legendpts={N} number of dots to put in the legend (default is 8). must be at least 2 −−squeeze={[0,1)} Y axis labels not fitting in the frame? squeeze the graph over with this. −−squeeze={[0,1),F} an amount to change the right margin can also be specified by F like this.