jam_mypie: Vectorized mypie() function for igraph vertex pie polygons

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

Vectorized mypie() function for igraph vertex pie polygons

Description

Vectorized mypie() function for igraph vertex pie polygons

Usage

jam_mypie(
  x,
  y,
  values,
  radius,
  edges = 200,
  col = NULL,
  angle = 45,
  density = NULL,
  border = NULL,
  frame.color = NULL,
  frame.lwd = par("lwd"),
  lty = NULL,
  lwd = par("lwd"),
  init.angle = 90,
  inner_pie_border = getOption("inner_pie_border", TRUE),
  inner_cex = 1.01,
  xy_max = NULL,
  overclose_polygons = FALSE,
  ...
)

Arguments

x, y	numeric coordinate for the center of each igraph node.
values	numeric vector of relative pie wedge sizes.
radius	numeric radius of pie
edges	integer number of edges to make a circle
col	character vector of R colors to fill each pie wedge, in order
angle, density	used to draw lines to fill each pie node, passed to polygon()
border	character vector of R colors for each pie wedge border
frame.color	character R color used around the entire pie circle.
lty	numeric or character line type
init.angle	numeric angle in degrees (0 to 360) where 0 is the top of the circle, proceeding clockwide.
inner_pie_border	logical whether to apply pie.border colors only along the inside of each pie wedge polygon, so that adjacent colors will be seen beside each other without overlapping adjacent borders. This method is currently in development.
overclose_polygons	logical indicating whether to close polygon coordinates with an extra couple points, to ensure the line join "ljoin" is properly called when drawing each polygon.
...	additional arguments are passed to polygon()

Details

This is a function called internally by shape.jampie.plot(), not intended for direct use.

See reorder_igraph_nodes() for visual examples.

This function is a light rewrite of igraph:::mypie(), except that this function determines polygon coordinates without drawing them, instead returns the polygon coordinates to the calling function shape.jampie.plot() which in turn draws all polygons once using the vectorized approach described for graphics::polygon().

See shape.jampie.plot() for more detail.

To disable pie.border set to NA with vertex.pie.border=NA or V(g)[[2]]$pie.border <- NA.

To disable frame.color set to NA with vertex.frame.color=NA or V(g)[2]$frame.color <- NA.

Value

data.frame with columns suitable for use in polygon() after each column is expanded to vector form. Columns x and y are stored AsIs() in list format, and should be combined with one NA value between each numeric vector. The NA values cause polygon() to draw a series of separate polygons in one vectorized step, much faster than drawing a series of polygons in an iterative loop.

See Also

Other jam igraph shapes: shape.coloredrectangle.plot(), shape.ellipse.clip(), shape.ellipse.plot(), shape.jampie.plot()

Examples

# See reorder_igraph_nodes() for visual examples.

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.