namesToColumns {idiogramFISH}

FUNCTION that modifies marks' names into columns

Description

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

Usage

 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 
)

Arguments

marksDf

data.frame with columns: markName,style,markPos

dfChrSize

data.frame, size of chr. Same of plot.

markType

character, use c("downArrow","upArrow","cM","cMLeft") or a subset

amountofSpaces

numeric, number of spaces for each column

colNumber

numeric, number of columns

protruding

numeric, same as plot, minimal protruding for arrow marks, equivalent to cM protruding

protrudingInt

numeric, spacing of columns in terms of width of chr. percent 1 = 100%. Defaults to 0.5

circularPlot

boolean, use TRUE for circular plots. Use FALSE otherwise

rotation

numeric, same as plot, anti-clockwise rotation, defaults to 0.5 which rotates chr. from top to -90 degrees. (-0.5*\pi )

defaultStyleMark

character, if some data in column style missing fill with this one. Defaults to "square"

orderChr

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

halfModDown

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

halfModUp

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

rotatMod

numeric, for circ. plots, when rotation != 0 (diff.), corrects alignment of labels. Defaults to 0

Value

data.frame