removeIgraphBlanks: Remove igraph blank wedges

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

Remove igraph blank wedges

Description

Remove igraph blank wedges

Usage

removeIgraphBlanks(
  g,
  blankColor = c("#FFFFFF", "#FFFFFFFF", "transparent"),
  c_max = 7,
  l_min = 95,
  alpha_max = 0.1,
  constrain = c("nrow", "ncol", "none"),
  resizeNodes = TRUE,
  applyToPie = TRUE,
  pie_to_circle = FALSE,
  pieAttrs = c("pie", "pie.value", "pie.names", "pie.color"),
  verbose = FALSE,
  ...
)

Arguments

g	igraph object containing one or more attributes from "pie.color" or "coloredrect.color".
blankColor	character vector of R colors directly matched to the input x vector. The value "transparent" is useful here, because it is not easily converted to HCL color space.
c_max	maximum chroma as determined by HCL color space, in range of no color 0 to maximum color 100.
l_min	numeric minimum luminance required for a color to be considered blank, combined with the c_max argument. This threshold prevents grey colors from being considered blank, unless their luminance is above this threshold.
alpha_max	numeric value indicating the alpha transparency below which a color is considered blank, in range of fully transparent 0, to fully non-transparent 1.
constrain	character value indicating for node shape "coloredrectangle" whether to constrain the "coloredrect.nrow" or "coloredrect.ncol" values. When "none" the nrow is usually dropped to nrow=1 whenever colors are removed.
resizeNodes	logical indicating whether to resize the resulting nodes to maintain roughly proportional size to the number of colored wedges.
applyToPie	logical indicating whether to apply the logic to nodes with shape "pie".
pie_to_circle	logical indicating whether node shapes for single-color nodes should be changed from "pie" to "circle" in order to remove the small wedge line in each pie node.
pieAttrs	character vector of vertex.attributes from g to be adjusted when applyToPie=TRUE. Note that "pie.color" is required, and other attributes are only adjusted when they are present in the input graph g.
verbose	logical indicating whether to print verbose output.
...	additional arguments are passed to isColorBlank().

Details

This function is intended to affect nodes with shapes "pie" or "coloredrectangle", and evaluates the vertex attributes "coloredrect.color" and "pie.color". For each node, any colors considered blank are removed, along with corresponding values in related vertex attributes, including ⁠"pie","pie.value","pie.names"⁠, ⁠"coloredrect.names","coloredrect.nrow","coloredrect.ncol","coloredrect.byrow"⁠.

This function calls isColorBlank() to determine which colors are blank.

This function is originally intended to follow igraph2pieGraph() which assigns colors to pie and coloredrectangle attributes, where missing values or values of zero are often given a "blank" color. To enhance the resulting node coloration, these blank colors can be removed in order to make the remaining colors more visibly distinct.

See Also

Other jam igraph functions: cnet2df(), cnet2im(), cnetplotJam(), cnetplot_internalJam(), color_edges_by_nodegroups(), color_edges_by_nodes_deprecated(), color_edges_by_nodes(), color_nodes_by_nodegroups(), communities2nodegroups(), drawEllipse(), edge_bundle_bipartite(), edge_bundle_nodegroups(), enrichMapJam(), fixSetLabels(), flip_edges(), get_bipartite_nodeset(), igraph2pieGraph(), jam_igraph(), jam_plot_igraph(), label_communities(), layout_with_qfrf(), layout_with_qfr(), mem2emap(), memIM2cnet(), mem_multienrichplot(), nodegroups2communities(), rectifyPiegraph(), relayout_with_qfr(), removeIgraphSinglets(), reorderIgraphNodes(), rotate_igraph_layout(), spread_igraph_labels(), subgraph_jam(), subsetCnetIgraph(), subset_igraph_components(), sync_igraph_communities(), with_qfr()

Examples

require(igraph);
g <- graph.full(n=3);
V(g)$name <- c("nodeA", "nodeB", "nodeC");
V(g)$shape <- "coloredrectangle";
V(g)$coloredrect.names <- split(
   rep(c("up","no", "dn"), 7),
   rep(V(g)$name, c(2,3,2)*3));
V(g)$coloredrect.byrow <- FALSE;
V(g)$coloredrect.nrow <- rep(3, 3);
V(g)$coloredrect.ncol <- c(2,3,2);
V(g)$label.degree <- pi*3/2;
V(g)$label.dist <- 3;
V(g)$size2 <- c(3, 3, 3);

color_v <- rep("white", 21);
color_v[c(1,3,7,9,15,19,20,21)] <- colorjam::rainbowJam(5);
V(g)$coloredrect.color <- split(
   color_v,
   rep(V(g)$name, c(2,3,2)*3));
par("mfrow"=c(2,2));
lg <- layout_nicely(g);
jam_igraph(g, layout=lg, use_shadowText=TRUE);

g2 <- removeIgraphBlanks(g, constrain="none");
V(g2)$size2 <- V(g2)$size2 / 3;
jam_igraph(g2, layout=lg, use_shadowText=TRUE,
   main="constrain='none'");

g3 <- removeIgraphBlanks(g, constrain="nrow");
jam_igraph(g3, layout=lg, use_shadowText=TRUE,
   main="constrain='nrow'");

g4 <- removeIgraphBlanks(g, constrain="ncol");
jam_igraph(g4, layout=lg, use_shadowText=TRUE,
   main="constrain='ncol'");

#
g7 <- graph.full(n=7);
V(g7)$coloredrect.color <- lapply(c(1,2,3,4,2,3,4),
   function(i){colorjam::rainbowJam(i)});
V(g7)$coloredrect.ncol <- c(1,1,1,1,2,3,4);
V(g7)$coloredrect.nrow <- c(1,2,3,4,1,1,1);
V(g7)$coloredrect.names <- V(g7)$coloredrect.color;
V(g7)$shape <- "coloredrectangle";
V(g7)$size <- 10;
V(g7)$size2 <- V(g7)$coloredrect.ncol * 1;
lg7 <- layout_nicely(g7);
jam_igraph(g7, layout=lg7,
   use_shadowText=TRUE,
   vertex.size2=5);

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