This function reads a data.frame with columns: chrName and
shortArmSize and longArmSize for monocentrics or a column chrSize for holocentrics and produces a plot of idiograms. If more
than one species, a column named OTU is needed.
Optionally, it reads another data.frame with the position of
marks (sites) dfMarkPos markpos, in which case a data.frame for mark characteristics
can be used dfMarkColor or a vector for mycolors
plotIdiograms(dfChrSize, dfMarkPos, dfCenMarks, dfMarkColor, mycolors,
markDistType = "beg", orderBySize = TRUE, centromereSize = 1,
chrWidth = 0.5, chrSpacing = 0.5, chrColor = "gray",
cenColor = "gray", roundness = 4, dotRoundCorr, karHeight = 2,
karHeiSpace = 2.5, karSepar = TRUE, amoSepar = 9,
chrId = "original", distTextChr = 1, indexIdTextSize = 1,
notesTextSize = 0.4, OTUTextSize = 1, legend = "aside",
markLabelSize = 1, markLabelSpacer = 1, chrIndex = TRUE,
nameChrIndexPos = 2, karIndex = TRUE, karIndexPos = 0.5,
notesPos = 0.5, morpho = TRUE, addOTUName = TRUE,
revOTUs = FALSE, ruler = TRUE, rulerPos = -0.5, rulerPosMod = 0,
ruler.tck = -0.02, rulerNumberPos = 0.5, rulerNumberSize = 1,
xlimLeftMod = 1, xlimRightMod = 2, ylimBotMod = 0.2,
ylimTopMod = 0.2, lwd.chr = 2, pattern = "",
addMissingOTUAfter = NA, missOTUspacings = 0, legendWidth = 1.7,
legendHeight = NA, Mb, MbThresholds = c(10000, 1000), ylabline = 0,
origin = "b", n = 50, notes, fixCenBorder = TRUE, MarkDistanceType,
propWidth = FALSE, useXYfactor = FALSE, ...)mandatory data.frame, with columns: OTU (optional), chrName (mandatory),
shortArmSize, longArmSize for monocen. or chrSize for holocen.
data.frame of marks (sites): cols: OTU (opt) chrName,
markName (name of site), chrRegion (for monocen), markDistCen (for monocen.),
markPos (for holocen.), markSize; column chrRegion:
use p for short arm, q for long arm and cen for centromeric mark; col. markDistCen: use distance from
centromere to mark, not necessary for cen. marks. See param. markDistType
data.frame, specific for centromeric marks. cols: chrName
and markName. See also dfMarkPos for another option to pass cen. marks
data.frame, optional, specifying colors and style for marks (sites);
cols: markName, markColor, style. style accepts: square or dots.
(if style missing all are plotted as square)
character vector, optional, i.e. c("blue","red","green") for specifying color of marks in order of appearance. if diverges with number of marks will be recycled if dfMarkColor present, mycolors will be ignored. To know the
order of your marks use something like: unique(c(dfMarkPos$markName,dfCenMarks$markName) )
character, if cen = the distance you provided is to
the center of the mark, if beg = the distance you provided is to the
beginning of the mark
logical value, when TRUE, sorts chromosomes by total
length from the largest to the smallest
numeric, this establishes the apparent size of cen in the plot in \(\mu\)m
numeric, relative chromosome width. Defaults to 0.5
numeric, horizontal spacing among chromosomes, see also chrWidth. Defaults to 0.5
character, main color for chromosomes
character, color for centromeres, if GISH use NULL
numeric, shape of vertices of chromosomes and square marks, higher values more squared
numeric, to be deprecated, requires useXYfactor=TRUE corrects roundness of dots and vertices of chromosomes. When style of sites = dots, an increase in this, makes the horizontal radius of the dot smaller. Use asp=1 instead
numeric, vertical size of karyotypes. See also karHeiSpace. Defaults to 2
numeric, vertical size of karyotypes including spacing. Proportional to karHeight, if overlap, increase
boolean, reduce distance among karyotypes FALSE = equally
sized karyotypes or TRUE = equally spaced karyotypes. Incompatible with addMissingOTUAfter
numeric, depends on karSepar=TRUE, if zero your
karyotypes will have no distance among them, if overlap,
increase this and karHeiSpace
character, print name of chromosome, "original" uses the original
name in OTU column of dfChrSize, "simple" (just 1 to ...) or "" (none).
numeric, distance from name of chromosome to chromosome,
also affects vertical separation of indices. Defaults to 1
numeric, font size of chr. and kar. indices and
chromosome name. Defaults to 1
numeric, font size of notes, see notes
numeric, font size of OTU name (species). Defaults to 1
character, "" for no legend; "inline" prints labels near
chromosomes; "aside" prints legend to the right of karyotypes (default). See markLabelSpacer
numeric, only if legend != (not) "", size of the text of
labels of marks (legend). Defaults to 1
numeric, only if legend="aside", space from the
rightmost chr. to legend. Defaults to 1
logical, add arm ratio and centromeric index
numeric, modify position of name of chr. indices
logical, add karyotype indices A (intrachromosomal - centromere pos.) and A2 (interchromosomal asymmetry, variation among chromosome sizes)
numeric, move karyotype index
numeric, move notes to the right
boolean, if TRUE prints the Guerra and Levan classif of cen.
position. see ?armRatioCI
boolean, if TRUE adds OTU (species) name to karyotype
boolean, The order of species is the one in the main
data.frame, use TRUE to reverse
boolean, display ruler to the left of karyotype, when FALSE no ruler
numeric, absolute position of ruler, corresponds to pos
argument of axis R plot
numeric, modify position of ruler, corresponds to line
argument of axis R plot
numeric, tick size of ruler, corresponds to tck argument of
axis R plot. Defaults to -0.02
numeric, modify position of numbers of ruler. Defaults to 0.5
numeric, size of number's font in ruler. Defaults to 1
numeric, modifies xlim left argument of plot
numeric, xlim right side modification by adding space to the right
of idiograms. Defaults to 2
numeric, modify ylim bottom argument of plot
numeric, modify ylim top argument of plot
thick of border of chr. and marks.
REGEX pattern to remove from names of marks
character, when you want to add space (ghost OTUs) after one or several OTUs, pass the names of OTUs preceding the desired space in a character vector i.e. c("species one","species five")
numeric, when you use addMissingOTUAfter this numeric vector should have the same length and corresponds to the number of free spaces (ghost OTUs) to add after each OTU respectively
factor to increase width of squares and of legend
factor to increase height of squares and dots of legend
deprecated, use MbThresholds
numeric vector of length 2. c(10000,1000). If chrSize > 10000 will be considered Mb. If markSize > 1000 will be considered Mb.
numeric, modify position of y axis title (Mb). See MbThresholds
For non-monocentric chr. (for holocentrics only) Use "b" if distance to mark in ("markPos" col. in "dfMarkPos") data.frame measured from bottom of chromosome, use "t" for distance to mark from top
numeric vertices number for round corners
data.frame, optional, with cols OTU and note for adding notes to each OTU, they appear to the right of chromosomes
boolean, use chr. color as centromere border color, see cenColor
deprecated, use markDistType
boolean, defaults to FALSE. Diminishes chr. width with increasing number of OTUs
boolean, for backwards compatibility, for using dotRoundCorr. Defaults to FALSE
accepts other arguments for the plot, such as, asp
plot
# NOT RUN {
data(dfOfChrSize)
plotIdiograms(dfOfChrSize)
plotIdiograms(dfChrSizeHolo)
# }
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