makedfMarkColorMycolors

This function reads character vector with marks names, a
character vector of
prohibited colors and a custom list of colors
to be associated with the mark names
It returns a data.frame with color and style for each mark

create

mark

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 

makedfMarkColorMycolors function

<dl><dt>markNames</dt>
<dd>names of marks</dd>
<dt>mycolors</dt>
<dd>character vector of names of colors</dd>
<dt>colorstoremove</dt>
<dd>character vector of colors to remove from mycolors. Default <code>NULL</code></dd>
<dt>defaultStyleMark</dt>
<dd>character vector with default style <code>"square"</code>. Other options: <code>"squareLeft"</code>, <code>"cM"</code>
<code>"cMLeft"</code>, <code>"dots"</code>, <code>"upArrow"</code>, <code>"downArrow"</code>, <code>"cenStyle"</code></dd></dl>

Arguments

FUNCTION to make a data.frame of Marks' characterisitcs — makedfMarkColorMycolors

<dl>

<dt>markNames</dt>
<dd>names of marks</dd>


<dt>mycolors</dt>
<dd>character vector of names of colors</dd>


<dt>colorstoremove</dt>
<dd>character vector of colors to remove from mycolors. Default <code>NULL</code></dd>


<dt>defaultStyleMark</dt>
<dd>character vector with default style <code>"square"</code>. Other options: <code>"squareLeft"</code>, <code>"cM"</code>
<code>"cMLeft"</code>, <code>"dots"</code>, <code>"upArrow"</code>, <code>"downArrow"</code>, <code>"cenStyle"</code></dd>

</dl>

makedfMarkColorMycolors: FUNCTION to make a data.frame of Marks' characterisitcs

Description

Usage

Value

Arguments