make_cnet_test: Make Cnet test igraph

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

Make Cnet test igraph

Description

Make Cnet test igraph

Usage

make_cnet_test(
  num_sets = 4,
  overlap_counts = c(57, 20, 12, 5),
  row_prefix = "",
  column_prefix = "Set",
  add_direction = TRUE,
  set_colors = NULL,
  seed = 123,
  repulse = 3.5,
  hide_solo_pie = TRUE,
  ...
)

Details

This function simply creates an igraph object with attributes expected for a cnet plot object:

• node attribute "nodeType" with values c("Gene", "Set").

It optionally derives random directionality when add_direction=TRUE, and calls apply_cnet_direction() so node borders are updated appropriately.

See Also

Other jam cnet igraph functions: adjust_cnet_nodeset(), adjust_cnet_set_relayout_gene(), apply_cnet_direction(), apply_nodeset_spacing(), get_cnet_nodeset(), nudge_igraph_node(), rotate_igraph_layout()

Examples

# by default, single-border-color pie is shown as circle
cnet1 <- make_cnet_test(border_lwd=2)
par("mar"=c(0, 0, 0, 0) + 0.5);
jam_igraph(cnet1, use_shadowText=TRUE)

# hide_solo_pie=FALSE shows every pie wedge bordder
cnet2 <- make_cnet_test(hide_solo_pie=FALSE, border_lwd=2)
jam_igraph(cnet2, use_shadowText=TRUE)

# Set nodes can be adjusted, reorienting the Gene nodes
cnet2_adj <- adjust_cnet_set_relayout_gene(cnet2,
   nodes=c("SetB", "SetD"),
   x=c(-0.1, 0), y=c(0, -0.2),
   repulse=3.6);
jam_igraph(cnet2_adj, use_shadowText=TRUE, label_dist_factor=0)

# nodeset spacing can be enforced
cnet3 <- make_cnet_test(num_sets=3)
jam_igraph(cnet3, use_shadowText=TRUE)
cnet3_sp <- apply_nodeset_spacing(cnet3,
   percent_spacing=7)
jam_igraph(cnet3_sp, use_shadowText=TRUE)

# a specific nodeset can be individually adjusted
cnet3_adj <- adjust_cnet_nodeset(cnet3_sp,
   set_nodes=list(c("SetA", "SetB")),
   x=c(-0.2), y=c(0.2))
jam_igraph(cnet3_adj, use_shadowText=TRUE)

# several nodesets can be adjusted at once
cnet3_adj2 <- adjust_cnet_nodeset(cnet3_sp,
   set_nodes=list("SetA,SetB", "SetA,SetC", "SetB,SetC"),
   x=c(-0.2, 0.2, 0), y=c(0.2, 0.2, -0.2))
jam_igraph(cnet3_adj2, use_shadowText=TRUE)

# individual nodes can be nudged
cnet3_adj2_nudge <- nudge_igraph_node(cnet3_adj2,
   nodes=c("T"), x=c(-0.02), y=c(0.1))
jam_igraph(cnet3_adj2_nudge, use_shadowText=TRUE, vertex.label.font=2)

# nodes can be nudged in larger sets using nodes_xy
cnet3_adj2_nudge2 <- nudge_igraph_node(cnet3_adj2,
   nodes_xy=list(
      T=c(-0.02, 0.2),
      AK=c(0.02, 0.2),
      AG=c(-0.2, 0),
      Q=c(0.2, 0)
))
jam_igraph(cnet3_adj2_nudge2, use_shadowText=TRUE, vertex.label.font=2)

jmw86069/jamenrich documentation built on Nov. 6, 2024, 7:07 p.m.