Chapter 14 Datasets

14.1 Chr. basic data Holo.

dfChrSizeHolo: Example data for holocentrics for 1 species

bigdfChrSizeHolo: Example data for holocentrics for several species, OTU

parentalAndHybHoloChrSize: Example data for holocentrics for several species, OTU

bigdfOfChrSize3Mb: Example data in Mb without chr. arms for three species, OTU

Format

data.frame with columns:

OTU grouping OTU (species), optional if only one OTU

chrName name of chromosome

chrSize size of chromosome, micrometers or Mb

group chromosome group, optional

chrNameUp optional name over kar.

Mbp optional name to show size in Mbp under kar., use only when chrSize is not in Mbp. To be used with chrSizeMbp=TRUE

14.2 Chr. basic data Monocen.

dfOfChrSize: Example data for monocentrics

bigdfOfChrSize: Example data for monocentrics for several species, OTU

humChr: Data for human karyotype, measured from Adler (1994)

allChrSizeSample: Example data for monocentrics for several species, OTU

parentalAndHybChrSize: Example data for monocentrics for GISH

traspadf: Example data for Tradescantia (Rhoeo) spathacea (Golczyk et al., 2005)

Format

data.frame with columns:

OTU species, optional if only one OTU (species)

chrName name of chromosome

shortArmSize size of short arm, micrometers

longArmSize size of long arm, micrometers

group chr group, optional

chrNameUp optional name over kar.

Mbp optional name to show size in Mbp, use only when shortArmSize is not in Mbp

14.3 Mark characteristics

Source: R/dfMarkStyle.R

style column does not apply to cen. marks, only color.

dfMarkColor: Example General data for marks NOT position

humMarkColor: human bands’ characteristics, from Adler (1994)

mydfMaColor: mark characteristics used in vignette of phylogeny

Format

dfMarkColor a data.frame with columns:

markName name of mark

markColor use R colors

style character, use square or dots, optional

protruding numeric, modifies aspect of cM/cMLeft marks, see parameter protruding in plotIdiograms, optional

14.4 Mark Positional data - Holocen.

Source: R/markdataholo.R

bigdfMarkPosHolo: Example data for mark position of holocentrics with column OTU

dfMarkPosHolo: Example data for mark position of holocentrics

dfAlloParentMarksHolo: Example data for mark position of GISH

bigdfOfMarks3Mb: Example data for mark position in Mb

Format

data.frame with columns:

OTU OTU, species, optional

chrName name of chromosome

markName name of mark

markPos position from bottom or top (see parameter origin in plotIdiograms)

markSize size of mark in micrometers or Mb

14.5 Mark Positional data - monocentrics

Source: R/markposDFs.R

bigdfOfMarks: Example data for mark position with column OTU

dfOfMarks: Example data for marks’ position

dfOfMarks2: Marks’ position including cen. marks

humMarkPos: human karyotype bands’ (marks) positions, measured from Adler (1994)

allMarksSample: Example data for marks’ position

dfAlloParentMarks: Example data for mark position of GISH of monocen.

traspaMarks: T. spathacea (Rhoeo) marks’ positions, from Golczyk et al. (2005)

Format

bigdfOfMarks a data.frame with columns:

OTU OTU, species, mandatory if in dfChrSize

chrName name of chromosome

markName name of mark

chrRegion use p for short arm, q for long arm, and cen for centromeric

markDistCen distance of mark to centromere (not for cen)

markSize size of mark (not for cen)

14.6 File eightSpIqtree.treefile

See chapter phylogeny (Nguyen et al., 2015)

14.7 File revBayesTutorial.tree

See chapter phylogeny (Höhna et al., 2017)