garfield.plot.fnx: Internal radial plotting function for the garfield.plot...
In garfield: GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

Description Usage Arguments Details Value Author(s) References See Also Examples

This function has been adapted from the 'radial.plot' function from the 'plotrix' package.

    garfield.plot.fnx(lengths, radial.pos = NULL, labels = NA, breaks = NA,
        label.pos = NULL, radlab = FALSE, start = 0, clockwise = FALSE,
        rp.type = "r", label.prop = 1.05, main = "", xlab = "", ylab = "",
        line.col = par("fg"), lty = par("lty"), lwd = par("lwd"),
        mar = c(2, 2, 3, 2), show.grid = TRUE, show.grid.labels = 4,
        show.radial.grid = TRUE, grid.col = "grey", grid.bg = "transparent",
        grid.left = FALSE, grid.unit = NULL, point.symbols = 1,
        point.col = par("fg"), show.centroid = FALSE, radial.lim = NULL,
        radial.labels = NULL, poly.col = NA, add = FALSE, ann.col = 1,
        ann.pch = 15, ann.col.mx = 1, compact = TRUE, ...)

`lengths`	A numeric data vector or matrix. If 'lengths' is a matrix, the rows will be considered separate data vectors.
`radial.pos`	A numeric vector or matrix of positions in radians. These are interpreted as beginning at the right (0 radians) and moving counterclockwise. If 'radial.pos' is a matrix, the rows must correspond to rows of 'lengths'.
`labels`	Character strings to be placed at the outer ends of the lines. If set to NA, will suppress printing of labels, but if missing, the radial positions will be used.
`breaks`	A vector of (potentially different) labels to 'labels' according to which to draw radial lines.
`label.pos`	The positions of the labels around the plot in radians.
`radlab`	Whether to rotate the outer labels to a radial orientation.
`start`	Where to place the starting (zero) point. Defaults to the 3 o'clock position.
`clockwise`	Whether to interpret positive positions as clockwise from the starting point. The default is counterclockwise.
`rp.type`	Whether to draw (r)adial lines, a (p)olygon, (s)ymbols or some combination of these. If 'lengths' is a matrix and rp.type is a vector, each row of 'lengths' can be displayed differently.
`label.prop`	The label position radius as a proportion of the maximum line length.
`main`	The title for the plot.
`xlab,ylab`	Normally x and y axis labels are suppressed.
`line.col`	The color of the radial lines or polygons drawn.
`lty`	The line type(s) to be used for polygons or radial lines.
`lwd`	The line width(s) to be used for polygons or radial lines.
`mar`	Margins for the plot. Allows the user to leave space for legends, long labels, etc.
`show.grid`	Logical - whether to draw a circular grid.
`show.grid.labels`	Whether and where to display labels for the grid - see Details.
`show.radial.grid`	Whether to draw radial lines to the plot labels.
`grid.col`	Color of the circular grid.
`grid.bg`	Fill color of above.
`grid.left`	Whether to place the radial grid labels on the left side.
`grid.unit`	Optional unit description for the grid.
`point.symbols`	The symbols for plotting (as in pch).
`point.col`	Colors for the symbols.
`show.centroid`	Whether to display a centroid.
`radial.lim`	The range of the grid circle. Defaults to 'pretty(range(lengths))', but if more than two values are passed, the exact values will be displayed.
`radial.labels`	Optional labels for the radial grid. The default is the values of radial.lim.
`poly.col`	Fill color if polygons are drawn. Use NA for no fill.
`add`	Whether to add one or more series to an existing plot.
`ann.col`	A vector of colours for symbols to be drawn on the outer circle.
`ann.pch`	A pch value for symbols to be drawn on the outer circle.
`ann.col.mx`	A matrix of colours for dots to be drawn on the outer circle, inside the symbols with 'ann.col' colours.
`compact`	A flag to specify if labels should be presented in a compact form or not.
`...`	Additional arguments are passed to 'plot'.

This function is only used internally as part of the garfield.plot function.

No value, but a plot is produced. See Details for further information.

Sandro Morganella <email: sm22@sanger.ac.uk>

Maintainer: Valentina Iotchkova <email: vi1@sanger.ac.uk>

Valentina Iotchkova, Graham Ritchie, Matthias Geihs, Sandro Morganella, Josine Min, Klaudia Walter, Nicholas Timpson, UK10K Consortium, Ian Dunham, Ewan Birney and Nicole Soranzo. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction. In preparation

garfield.plot, garfield.run, garfield

DATA = rbind(rnorm(10,5,0.5),rnorm(10,3.5,0.5),rnorm(10,2,0.5))
garfield.plot.fnx(DATA,ann.col.mx=DATA!=0, ann.col=rep(1:2,each=5),
    ann.pch=15, rp.type="p",line.col=1:3,show.grid=TRUE, show.radial.grid=TRUE,
    labels=paste("label ",c(1:10)," ",sep=""),breaks=(1:10), radlab=TRUE, 
    poly.col=1:3)