shape.jampie.plot: custom igraph vertex shape jampie

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

custom igraph vertex shape jampie

Description

custom igraph vertex shape jampie

clip function for igraph vertex shape jampie

Usage

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

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

Details

This function is a vectorized replacement for plotting vertex shape "pie" in much more efficient manner.

It is substantially faster to use shape.jampie.plot() than default igraph plotting, even for only 20 pie nodes, the speed becomes even more dramatically faster for larger networks with 200+ nodes. Minutes reduced to 1-2 seconds rendering time.

Pie nodes with only one large 100% wedge no longer display the small line from origin, which is a change and improvement from default igraph rendering.

Attribute vertex.pie.border can be used to draw a border around each pie wedge, for each node. It should be a list with lengths(vertex.pie.border) equal to lengths(vertex.pie). To disable, use pie.border=NA on the entire attribute, or individual nodes.

Attribute vertex.frame.color can be used to draw a single circular border around the entire pie node. The length(vertex.frame.color) should equal the number of nodes in the graph, for example determined with igraph::vcount(g). Note that frame.color is drawn for each node after the pie wedges, on top of pie.border if defined, so it is recommended to use only one form of border for each node.

Each pie node is drawn completely, in order: pie wedges including optional pie.border outline for each pie wedge, then frame.color around the entire node circle; then the next pie node is drawn. This ordering ensures each entire pie node will overlap, or be overlapped by other nodes, without artifacts of the frame.color being shown on top of pie nodes that are otherwise beneath visibility.

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.

This function defines the clipping function for custom igraph vertex shape jampie.

See Also

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

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

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", "dodgerblue3");
vseq <- seq_len(igraph::vcount(g1));
vsizes <- c(3, 2, 2, 2, 1);
igraph::V(g1)$pie <- lapply(vseq, function(i){
   rep(1, vsizes[i])
})
set.seed(1);
igraph::V(g1)$pie.border <- lapply(vseq, function(i){
   sample(colorset,
      replace=TRUE,
      size=vsizes[i])
})
igraph::V(g1)$pie.color <- lapply(vseq, function(i){
   jamba::alpha2col(alpha=0.5,
      igraph::V(g1)$pie.border[[i]])
})
igraph::V(g1)$pie.lwd <- rep(5, igraph::vcount(g1))
igraph::V(g1)$frame.lwd <- c(2, 1, 1, 1, 1)*2;
igraph::V(g1)$frame.color <- NA
igraph::V(g1)$size <- c(45, 25, 25, 25, 25);
igraph::V(g1)$shape <- "jampie";

par("mar"=c(2, 2, 3, 2))
igraph::plot.igraph(g1, vertex.label="",
   vertex.shape="pie", vertex.frame.color="grey45",
   main="shape='pie'\nigraph::plot.igraph()")

jam_igraph(g1, vertex.label="",
   main="shape='jampie', frame.color=NA\njam_igraph()")


jam_igraph(g1, vertex.label="",
   vertex.frame.lwd=2,
   main="shape='jampie', frame.color='black'\njam_igraph()",
   vertex.shape="jampie", vertex.frame.color="black")

jam_igraph(g1, vertex.label="", vertex.frame.color="black")

# print pie.color data
print(igraph::vertex_attr(g1)$pie.color);

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