checkNameChrDfMarks

This function reads two data.frames the one with chromosome sizes, and one df
with data of marks (sites) both have to have the column <code>chrName</code> and if
several species, <code>OTU</code>. The functions returns a filtered list with 1.
data.frame of
chrSizes,
2. data.frame of marks, 3. mark names 4. max mark size.

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 

checkNameChrDfMarks function

<dl><dt>listChrSize</dt>
<dd>list of data.frames, with columns: OTU (optional),
chrName, for chr.
with cen.: shortArmSize, longArmSize, for holoc.: chrSize</dd>
<dt>listOfdfMarks</dt>
<dd>list of data.frames of marks (sites): OTU (opt /
mandat. if in
dfChrSize), chrName markName markSize, for chr. with cen.: chrRegion (p,q)
markDistCen, for holoc: markPos</dd></dl>

Arguments

Function to check names of OTUs (species) among data.frames — checkNameChrDfMarks

<dl>

<dt>listChrSize</dt>
<dd>list of data.frames, with columns: OTU (optional),
chrName, for chr.
with cen.: shortArmSize, longArmSize, for holoc.: chrSize</dd>


<dt>listOfdfMarks</dt>
<dd>list of data.frames of marks (sites): OTU (opt /
mandat. if in
dfChrSize), chrName markName markSize, for chr. with cen.: chrRegion (p,q)
markDistCen, for holoc: markPos</dd>

</dl>

checkNameChrDfMarks: Function to check names of OTUs (species) among data.frames

Description

Usage

Value

Arguments