plotSqMarks

internal

Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).

Fernando Roa

idiogramFISH

Shiny App. Idiograms with Marks and Karyotype Indices

Mariana PC Telles 

plotSqMarks function

<dl><dt>circularPlot</dt>
<dd>boolean TRUE for circ.</dd>
<dt>squareness</dt>
<dd>squareness of vertices &lt;</dd>
<dt>dfMarkColorInt</dt>
<dd>colors for marks</dd>
<dt>listMarkPosSq</dt>
<dd>list of df. of mark pos.</dd>
<dt>listChrSize</dt>
<dd>chr size df list</dd>
<dt>specialChrWidth</dt>
<dd>numeric, width of chr.</dd>
<dt>chrWidth</dt>
<dd>numeric, width of chr.</dd>
<dt>yfactor</dt>
<dd>yMark distortion based on canvas proportion</dd>
<dt>y</dt>
<dd>list, y coords.</dd>
<dt>markLabelSize</dt>
<dd>numeric, font size</dd>
<dt>pattern</dt>
<dd>character, regex</dd>
<dt>separFactor</dt>
<dd>numeric, sep. kars.</dd>
<dt>labelSpacing</dt>
<dd>numeric, spacing</dd>
<dt>circleCenter</dt>
<dd>numeric</dd>
<dt>circleCenterY</dt>
<dd>numeric</dd>
<dt>radius</dt>
<dd>numeric</dd>
<dt>legend</dt>
<dd>character</dd>
<dt>rotation</dt>
<dd>rotate</dd>
<dt>labelOutwards</dt>
<dd>srt</dd></dl>

Arguments

sqPlotMarkCP
This is an internal function that plot marks — plotSqMarks

<dl>

<dt>circularPlot</dt>
<dd>boolean TRUE for circ.</dd>


<dt>squareness</dt>
<dd>squareness of vertices &lt;</dd>


<dt>dfMarkColorInt</dt>
<dd>colors for marks</dd>


<dt>listMarkPosSq</dt>
<dd>list of df. of mark pos.</dd>


<dt>listChrSize</dt>
<dd>chr size df list</dd>


<dt>specialChrWidth</dt>
<dd>numeric, width of chr.</dd>


<dt>chrWidth</dt>
<dd>numeric, width of chr.</dd>


<dt>yfactor</dt>
<dd>yMark distortion based on canvas proportion</dd>


<dt>y</dt>
<dd>list, y coords.</dd>


<dt>markLabelSize</dt>
<dd>numeric, font size</dd>


<dt>pattern</dt>
<dd>character, regex</dd>


<dt>separFactor</dt>
<dd>numeric, sep. kars.</dd>


<dt>labelSpacing</dt>
<dd>numeric, spacing</dd>


<dt>circleCenter</dt>
<dd>numeric</dd>


<dt>circleCenterY</dt>
<dd>numeric</dd>


<dt>radius</dt>
<dd>numeric</dd>


<dt>legend</dt>
<dd>character</dd>


<dt>rotation</dt>
<dd>rotate</dd>


<dt>labelOutwards</dt>
<dd>srt</dd>

</dl>

plotSqMarks: sqPlotMarkCP This is an internal function that plot marks

Description

Usage

Value

Arguments