arcplot: Arc Diagram Plot

In REIDS: Random Effects for the Identification of Differential Splicing

Description

Give me an edgelist and I'll help you plot a pretty damn arc diagram

Usage

arcplot(edgelist, vertices, sorted = FALSE, decreasing = FALSE,
  ordering = NULL, labels = NULL, horizontal = TRUE, above = NULL,
  col.arcs = "#5998ff77", lwd.arcs = 1.8, lty.arcs = 1, lend = 1,
  ljoin = 2, lmitre = 1, show.nodes = TRUE, pch.nodes = 19,
  cex.nodes = 1, col.nodes = "gray80", bg.nodes = "gray80",
  lwd.nodes = 1, show.labels = TRUE, col.labels = "gray55",
  cex.labels = 0.9, las = 2, font = 1, line = 0, outer = FALSE,
  adj = NA, padj = NA, axes = FALSE, ...)

Arguments

edgelist	basically a two-column matrix with edges
vertices	optional vector of vertex names corresponding with those in the edgelist
sorted	logical to indicate if nodes should be sorted (default FALSE)
decreasing	logical to indicate type of sorting (used only when sorted=TRUE)
ordering	optional numeric or string vector providing the ordering of nodes. When provided, this parameter overrides sorted=TRUE). See the details section for more information.
labels	optional string vector with labels for the nodes
horizontal	logical indicating whether to plot in horizontal orientation
above	optional vector indicating which arcs should be displayed above (or to the right) and below (or to the left) of the axis
col.arcs	color for the arcs (default "gray50")
lwd.arcs	line width for the arcs (default 1)
lty.arcs	line type for the arcs (see par)
lend	the line end style for the arcs (see par)
ljoin	the line join style for the arcs (see par)
lmitre	the line mitre limit for the arcs (see par)
show.nodes	logical indicating whether to show node symbols
pch.nodes	plotting 'character', i.e. symbol to use when plotting nodes (pch.nodes=0:25)
cex.nodes	expansion of the node symbols (default 1)
col.nodes	color of the node symbols (default "gray50")
bg.nodes	background (fill) color for the node symbols given by pch.nodes=21:25
lwd.nodes	line width for drawing node symbols (see points)
show.labels	logical indicating whether to show node labels
col.labels	color of the node labels (default "gray50")
cex.labels	expansion of node labels (default "gray50")
las	numeric in 0,1,2,3; the style of axis labels (see par)
font	font used for node labels (see par)
line	on which margin line the node labels are displayed, starting at 0 counting outwards (see mtext)
outer	use outer margins, if available, to plot node labels (see mtext)
adj	adjustment for each string in reading direction (see mtext)
padj	adjustment for each string perpendicular to the reading direction (see mtext)
axes	logical indicating whether to plot the axes (default FALSE)
...	further graphical parameters (see par), including family, xpd, main, asp, etc.

Details

The arcs are scaled such that they fit in a plot region with its x-axis ranging from zero to one. Node symbols and labels can be optionally displayed. Node symbols are displayed through the function points. In turn, node labels are displayed through the function mtext.

When ordering is provided in numeric format and node labels are strings, the labels are alphabetically ordered first, and then nodes are sorted according to the provided ordering.

If ordering is provided in string format, the node labels must be strings as well. The nodes will be sorted according to ordering.

Author(s)

Gaston Sanchez

REIDS documentation built on May 2, 2019, 6:42 a.m.