checkNameChrDfMarks

list of data.frames, with columns: OTU (optional),
chrName, for chr.
with cen.: shortArmSize, longArmSize, for holoc.: chrSize

listOfdfChromSize

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

listOfdfMarks

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 (when not circular). Supports micrometers, cM and Mb or any unit. Two styles of centromeres are available: triangular and rounded; and six styles of marks: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow, downArrow; 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).

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

Description

Usage

Arguments

Value