shape.coloredrectangle.plot: custom igraph vertex shape coloredrectangle
In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

shape.coloredrectangle.plot

R Documentation

custom igraph vertex shape coloredrectangle

Description

custom igraph vertex shape coloredrectangle

Usage

shape.coloredrectangle.plot(coords, v = NULL, params)

shape.coloredrectangle.clip(coords, el, params, end = c("both", "from", "to"))

Arguments

`coords`	two-column numeric matrix with x- and y-coordinates, respectively.
`v`	optional ids of the vertices to plot. It should match the number of rows in the `coords` argument.
`params`	a function object that can be called to query vertex/edge/plot graphical parameters. The first argument of the function is `'vertex'`, `'edge'` or `'plot'` to decide the type of the parameter, the second is a character string giving the name of the parameter.

Details

This function defines the plotting function for custom igraph vertex shape coloredrectangle. The coloredrectangle shape is described as:

Each vertex is drawn as a rectangle, filled with squares which are each individually colored.
The squares are arrayed into a number of columns and rows, which are defined for each vertex using coloredrect.ncol and coloredrect.nrow, respectively.
The vector of colors is arrayed as values of a matrix, therefore coloredrect.byrow is logical to indicate whether colors should fill the matrix by row, similar to how byrow=TRUE is used.
The colors for each vertex are defined by coloredrect.color, which is a list of character color vectors. When coloredrect.color does not exist, values from pie.color will be used if they exist.
Any missing colors are displayed as NA which applies no color. For example, when a vertex has 3 columns, 2 rows, and only 5 colors, the colors are not recycled. Instead, the last color is NA to render no color in that position.
Each square may also have an optional border, defined by coloredrect.border, coloredrect.lwd, and coloredrect.lty. These borders are drawn as inner borders so they do not overlap optional frame border.
Each node may have a frame border, defined by frame.color, frame.lwd, and frame.lty. The frame border is drawn as an outer border so it does not overlap inner borders, adding some height and width to the final node. The frame border is drawn before the node squares are drawn.
The size of each square inside the rectangle is defined by size2, such that the rectangle width is coloredrect.ncol * size2 and the rectangle height is coloredrect.nrow * size2.
Node sizes may be adjusted by enabling equalize_sizes in one of two ways:
1. options(coloredrectangle.equalize_sizes=TRUE) (priority); or
2. vertex.coloredrect.equalize_sizes=TRUE, which is equivalent to igraph::V(g)$coloredrect.equalize_sizes=TRUE. in the latter case, only the first value is recognized.
The behavior of equalize_sizes is described below:
- equalize_sizes=FALSE (default), nodes are exactly size2 multiples of coloredrect.ncol and coloredrect.nrow.
- equalize_sizes=TRUE or 1, the shortest side of each node is scaled to size2. This option is useful to ensure nodes are never smaller than size2 width or height, but can be larger.
- equalize_sizes=2, the longest side of each node is scaled to size2. This option is useful to ensure nodes fit insides a square with size2 sides.
Nodes are drawn using vectorized processes where possible. However, the primary function graphics::symbols() only permits vectorized plotting for one lwd/lty combination at a time, so rendering is split into unique combinations of lwd/lty. Vectorized rendering is substantially faster than iterative rendering, and the majority of circumstances uses only one lwd/lty combination for all nodes. Line width is not an optimal way to convey a quantitative measurement, however it can be useful to highlight particular nodes of interest.
When coloredrect.ncol does not exist, the ncol will be defined by allowing up to two rows by default, enough to accommodate the number of colors in coloredrect.color.
When coloredrect.ncol * coloredrect.nrow will not fit all colors in coloredrect.color, the coloredrect.ncol will be extended to create enough positions to display all colors.
When coloredrect.nrow does not exist, it will use a value based upon coloredrect.ncol and the length of coloredrect.color.

The values coloredrect.color and other variables described above refer to igraph vertex attributes, and can be accessed for a given igraph object g as follows:

igraph::V(g)$coloredrect.color
igraph::vertex_attr(g, "coloredrect.color")
or during plotting the value can be defined using the syntax igraph::plot(g, vertex.coloredrect.color=list(...))

Note that blank positions inside coloredrectangle nodes can be removed via removeIgraphBlanks(), which also has the effect of modifying the coloredrect.ncol and coloredrect.nrow, by applying the appropriate logic.

Todo: The clip function should adjust the node boundary to account for frame.color and frame.lwd when present, since the frame is drawn as an outer border and slightly increases the size of the node.

Value

the plot function returns an invisible list of data.frame objects which were used to draw the rectangle objects. However the purpose of this function is the by-product that it draws rectangles onto an igraph graph. The clip function returns coordinates corresponding to the outer node edge based upon argument end:

end="both" returns 4 columns, the x,y 'edge from' and x,y 'edge to' coordinates, respectively
end="from" returns 2 columns, the x,y 'edge from' coordinates
end="to" returns 2 columns, the x,y 'edge to' coordinates

Examples

# prepare example igraph object
am <- matrix(ncol=5, nrow=5,
   data=0,
   dimnames=list(LETTERS[1:5], LETTERS[1:5]))
am[2:5, 1] <- 1;
g1 <- igraph::graph_from_adjacency_matrix(am)
igraph::graph_attr(g1, "layout") <- cbind(x=c(0, 1, 1, -1, -1),
   y=c(0, 1, -0.5, 0.5, -1))
colorset <- c("firebrick3", "gold", "deepskyblue",
   "mediumpurple3", "orchid1")
colorset <- c("firebrick3", "dodgerblue3");
vseq <- seq_len(igraph::vcount(g1));
vsizes <- c(3, 2, 2, 2, 1);
set.seed(1);
igraph::V(g1)$coloredrect.border <- lapply(vseq, function(i){
   sample(colorset,
      replace=TRUE,
      size=vsizes[i])
})
igraph::V(g1)$coloredrect.color <- lapply(vseq, function(i){
   jamba::alpha2col(alpha=0.5,
      igraph::V(g1)$coloredrect.border[[i]])
})
igraph::V(g1)$coloredrect.ncol <- c(2, 2, 2, 1, 1);
igraph::V(g1)$coloredrect.nrow <- c(2, 1, 1, 2, 1);
igraph::V(g1)$coloredrect.lwd <- rep(3, igraph::vcount(g1))
igraph::V(g1)$frame.lwd <- c(2, 1, 1, 1, 1);
igraph::V(g1)$frame.color <- "black"
igraph::V(g1)$size2 <- 10;
igraph::V(g1)$shape <- "coloredrectangle";

plot(g1, vertex.label="")
title(font.main=1, line=1.5, main=paste0(
   "Each square is consistent size by vertex.size2\n"))
title(font.main=1, cex.main=1, line=0.5, main=paste0(
   "'vertex.coloredrect.equalize_sizes=FALSE' or\n",
   "'options(coloredrectangle.equalize_sizes=FALSE'"))

# equalize shortest side to size2
plot(g1, vertex.label="", vertex.coloredrect.equalize_sizes=TRUE)
title(font.main=1, line=1.5, main=paste0(
   "The shortest side is fixed by vertex.size2\n"))
title(font.main=1, cex.main=1, line=0.5, main=paste0(
   "'vertex.coloredrect.equalize_sizes=TRUE' or\n",
   "'options(coloredrectangle.equalize_sizes=TRUE'"))

# equalize longest side to size2
plot(g1, vertex.label="", vertex.coloredrect.equalize_sizes=2)
title(font.main=1, line=1.5, main=paste0(
   "The longest side is fixed by vertex.size2\n"))
title(font.main=1, cex.main=1, line=0.5, main=paste0(
   "'vertex.coloredrect.equalize_sizes=2' or\n",
   "'options(coloredrectangle.equalize_sizes=2'"))

jmw86069/jamenrich documentation built on Feb. 3, 2024, 12:40 p.m.