perMark

calculates fraction (%) of chromosome for each mark

chromosome

percentage

span

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 

perMark function

<dl><dt>dfMarkPos</dt>
<dd>data.frame, of marks' position</dd>
<dt>listOfdfChromSize</dt>
<dd>list of data.frames or data.frame of chr. sizes.</dd>
<dt>result</dt>
<dd>character, type of return, <code>"data.frame"</code> or <code>"list"</code></dd>
<dt>bToRemove</dt>
<dd>character vector, bands to ignore</dd></dl>

Arguments

FUNCTION perMark — perMark

<dl>

<dt>dfMarkPos</dt>
<dd>data.frame, of marks' position</dd>


<dt>listOfdfChromSize</dt>
<dd>list of data.frames or data.frame of chr. sizes.</dd>


<dt>result</dt>
<dd>character, type of return, <code>"data.frame"</code> or <code>"list"</code></dd>


<dt>bToRemove</dt>
<dd>character vector, bands to ignore</dd>

</dl>

perMark: FUNCTION perMark

Description

Usage

Value

Arguments

Examples