namesToColumns: FUNCTION that modifies marks' names into columns
In idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

namesToColumns

R Documentation

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`