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.IX Title "REPEATVIZ 1"
.TH REPEATVIZ 1 2024-11-09 "perl v5.40.0" "User Contributed Perl Documentation"
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.SH NAME
repeatviz.pl \-\- visualize a bunch of repeats using graphviz
.SH SYNOPSIS
.IX Header "SYNOPSIS"
repeatviz.pl <input> [output]
.SH OPTIONS
.IX Header "OPTIONS"
output is defined based on the input name unless otherwise specified
.PP
.Vb 10
\& 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\*(Aqs color generator}
\&\-\-connect draw connecting edges for points in  adjacent sequences
\&\-\-maxlines={N} don\*(Aqt 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.
.Ve