garfield.plot.fnx {garfield} | R Documentation

## Internal radial plotting function for the garfield.plot function

### Description

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

### Usage

        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, ...)

### Arguments

`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'.

### Details

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

### Value

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

### Author(s)

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

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

### References

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

### See Also

`garfield.plot`, `garfield.run`, `garfield`

### Examples

    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)

[Package garfield version 1.18.0 Index]