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Make Cnet test igraph

Source: R/jamenrich-make-cnet-test.R
make_cnet_test.Rd

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,
  ...
)

Arguments

num_sets

integer number of sets, default 4.

overlap_counts

integer vector of counts, with length 'num_sets', default 'c(57, 20, 12, 5)'.

row_prefix

character default "" used as a prefix for rows names.

column_prefix

character default "Set" used as a prefix for set names.

add_direction

logical default TRUE, whether to include direction.

set_colors

character vector of colors per set.

seed

numeric used to fix the random seed.

repulse

numeric default 3.5, passed to layout_with_qfr().

hide_solo_pie

logical default TRUE, passed to mem2cnet().

...

additional arguments are passed to mem2cnet().

Value

igraph object containing Cnet concept network data, specifically with vertex attribute 'nodeType' with values 'Gene' or 'Set'.

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 utilities: adjust_cnet_nodeset(), adjust_cnet_set_relayout_gene(), apply_nodeset_spacing(), bulk_cnet_adjustments(), get_cnet_nodeset(), launch_shinycat()

Examples

# by default, single-border-color pie is shown as circle
cnet1 <- make_cnet_test(border_lwd=2)
withr::with_par(list("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)
withr::with_par(list("mar"=c(0, 0, 0, 0) + 0.5),{
   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);
withr::with_par(list("mar"=c(0, 0, 0, 0) + 0.5),{
   jam_igraph(cnet2_adj, use_shadowText=TRUE, label_dist_factor=0)
})


# nodeset spacing can be enforced
cnet3 <- make_cnet_test(num_sets=3)
withr::with_par(list("mar"=c(0, 0, 0, 0) + 0.5),{
   jam_igraph(cnet3, use_shadowText=TRUE)
})

cnet3_sp <- apply_nodeset_spacing(cnet3,
   percent_spacing=7)
withr::with_par(list("mar"=c(0, 0, 0, 0) + 0.5),{
   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))
withr::with_par(list("mar"=c(0, 0, 0, 0) + 0.5),{
   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))
withr::with_par(list("mar"=c(0, 0, 0, 0) + 0.5),{
   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))
withr::with_par(list("mar"=c(0, 0, 0, 0) + 0.5),{
   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)
))
withr::with_par(list("mar"=c(0, 0, 0, 0) + 0.5),{
   jam_igraph(cnet3_adj2_nudge2, use_shadowText=TRUE, vertex.label.font=2)
})