Reads a data.frame with marks' of styles
downArrow,upArrow,cM,cMLeft
positions. It separates names in columns, avoiding overlap when multiple
close names
Exceptionally this function requires the column style in the data.frame of marks' positions.
Returns a data.frame
namesToColumns( marksDf, dfChrSize, markType = c("downArrow", "upArrow",
"cMLeft", "cM"), amountofSpaces = 13, colNumber = 2, protruding = 0.2,
protrudingInt = 0.5, circularPlot = TRUE, rotation = 0.5,
defaultStyleMark = "square", orderChr = "size", halfModDown = NA,
halfModUp = NA, rotatMod = 0
)data.frame with columns: markName,style,markPos
data.frame, size of chr. Same of plot.
character, use
c("downArrow","upArrow","cM","cMLeft") or a subset
numeric, number of spaces for each column
numeric, number of columns
numeric, same as plot, minimal protruding for arrow marks, equivalent to cM protruding
numeric, spacing of columns in terms of width of chr.
percent 1 = 100%.
Defaults to 0.5
boolean, use TRUE for circular plots. Use
FALSE otherwise
numeric, same as plot, anti-clockwise rotation, defaults to
0.5 which
rotates chr. from top to -90 degrees. (-0.5*\(\pi\) )
character, if some data in column style missing
fill with this one.
Defaults to "square"
character, replaces orderBySize - deprecated when "size", sorts chromosomes by total
length from the largest to the smallest. "original": preserves d.f. order. "name":
sorts alphabetically; "group": sorts by group name
numeric, for circ. plots, when plotting several
chromosomes in a circular
plot, using a small value 0.05 corrects for alignment problems of
downArrows,
cMLeft labels. Defaults to NA
numeric, for circ. plots, when plotting several
chromosomes in a circular
plot, using a small value 0.05 corrects for alignment problems of
upArrows, cM
labels. Defaults to NA
numeric, for circ. plots, when rotation != 0 (diff.),
corrects alignment of
labels. Defaults to 0
data.frame