This function reads a dataframe with columns: chrName
and chrSize and plots as idiograms. If more than one species, a column
named OTU is needed. Accepts micrometers and Mb.
Optionally, it reads another dataframe with the position of
marks (sites) dfMarkPos, in that case the description of marks is
necessary in dataframe dfMarkColor
plotIdiogramsHolo(dfChrSize, dfMarkPos, dfMarkColor, mycolors,
MarkDistanceType = "beg", origin = "b", orderBySize = TRUE,
Mb = FALSE, ylabline = 0, chrWidth = 1.5, chrSpacing = 1.5,
chrColor = "gray", roundness = 4, dotRoundCorr = 1.5,
karHeight = 1.2, karSpacing = 1.6, reduDistKar = TRUE,
reduDistKarTol = 9, chrId = "original", distTextChr = 0.3,
indexIdTextSize = 0.4, OTUTextSize = 0.6, legend = "inline",
markLabelSize = 0.4, markLabelSpacer = 2, lwd.chr = 1,
karIndex = TRUE, karIndexPos = 0.5, addOTUName = TRUE,
revOTUs = FALSE, ruler = TRUE, rulerPos = -0.5, rulerPosMod = 0,
ruler.tck = -0.004, rulerNumberPos = 0.2, rulerNumberSize = 0.4,
xlimLeftMod = 1, xlimRightMod = 10, ylimBotMod = 0.2,
ylimTopMod = 0.2, addMissingOTUAfter = NA, missOTUspacings = 0,
legendWidth = 1.75, ...)dataframe with columns: OTU (optional), chrName, chrSize (see Mb)
dataframe of marks (sites): cols: OTU (opt) chrName, markName (name of site), markPos, markSize
dataframe specifying colors for marks (sites); cols: markName, markColor, style: square or dots
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(dfMarkPos$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
use "b" if distance to mark (markPos col. in dfMarkPos) measured from bottom, use "t" for distance to mark from top
logical value, when TRUE, sorts chromosomes by total length from the largest to the smallest
boolean, if TRUE distance in dfs is not micrometers but bases, will be shown as Megabases
numeric if Mb=TRUE modify position of y axis title (Mb)
numeric, chromosome width
numeric, horizontal spacing among chromosomes
character, main color for chromosomes
numeric, shape of vertices of chromosomes and square marks, higher values more squared
numeric, correct roundness of dots and vertices of chromosomes. When style of sites = dots, an increase in this, makes the horizontal radius of the dot smaller
numeric, vertical size of karyotypes
numeric, proportional to karHeight for spacing of karyotypes, y axis, if overlap, increase
boolean, reduce distance among karyotypes FALSE = equally sized karyotypes or TRUE= equally spaced karyotypes
numeric, depends on reduDistKar=TRUE, if zero your karyotypes will have no distance among them, use 1 to 11, if overlap, increase this and karSpacing
character, print name of chromosme, "original" uses the original name in OTU column of dfChrSize, "simple" (just 1 to ...) or "" (none).
numeric, distance from name of chromosome to chromosome
numeric, font size of chromosome name and A2 index
numeric, font size of OTU name (species)
character, "" for no legend; "inline" prints labels near chromosomes; "aside" prints legend to the right of karyotypes
numeric, only if legend !="", size of the text of labels of marks (legend)
numeric, only if legend !="", space from the rightmost chr. to legend
numeric, thick of border of chr. or marks
logical, add karyotype index A2 (interchromosomal asymmetry, variation among chromosome sizes)
numeric, move karyotype index
boolean, if TRUE adds OTU (species) name to karyotype
boolean, The order of species is the one in the main dataframe, 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
numeric, modify position of numbers of ruler
numeric, size of number's font in ruler
numeric, modifies xlim left parameter of plot
numeric, xlim modification by adding space to the right of idiograms
numeric, modify ylim bottom parameter of plot
numeric, modify ylim top parameter of plot
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 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 boxes of legend
accepts other arguments for the plot, such as, asp
plot
plotIdiograms
# NOT RUN {
data(dfChrSizeHolo)
plotIdiogramsHolo(dfChrSizeHolo)
# }
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