plot_full_network {cape}

Plot the final epistatic network in a traditional network view.

Description

This function plots the final results in a layout different to both plot_variant_influences and plot_network. In this view, the network is plotted with a traditional network layout. The genomic position information in plot_network is lost, but in this view it is easier to see the structure of the overall network in terms of hubs and peripheral nodes. In this view, each node is plotted as a pie-chart, and the main effects of the node are indicated as positive, negative, or not-significant (gray). Significant interactions are shown arrows between nodes and colored based on whether they are positive or negative interactions. Colors for positive and negative main effects and interactions are specified in the arguments. The function get_network must be run before plotting the network.

Usage

plot_full_network(
  data_obj,
  p_or_q = 0.05,
  collapsed_net = TRUE,
  main = NULL,
  color_scheme = c("DO/CC", "other"),
  pos_col = "brown",
  neg_col = "blue",
  bg_col = "gray",
  light_dark = "f",
  node_border_lwd = 1,
  layout_matrix = NULL,
  zoom = 1,
  xshift = 0,
  yshift = 0,
  node_radius = 1,
  label_nodes = TRUE,
  label_offset = 0,
  label_cex = 1,
  legend_radius = 1,
  legend_cex = 1,
  legend_position = "topleft",
  arrow_offset = node_radius,
  arrow_length = 0.2,
  edge_lwd = 2
)

Arguments

data_obj

A Cape object

p_or_q

The maximum p value (or q value if FDR was used) for significant main effects and interactions.

collapsed_net

A logical value indicating whether to show the network condensed into linkage blocks (TRUE) or each individual marker (FALSE)

main

A title for the plot

color_scheme

either "DO/CC" or "other". "DO/CC" uses the official "DO/CC" colors for the DO/CC alleles http://www.csbio.unc.edu/CCstatus/index.py?run=AvailableLines.information "other" uses an unrelated color palette for multiple alleles.

pos_col

The color to use for positive main effects and interactions must be one of "green", "purple", "red", "orange", "blue", "brown", "yellow", "gray" see get_color

neg_col

The color to use for negative main effects and interactions takes the same values as pos_col.

bg_col

The color to be used in pie charts for non-significant main effects. Takes the same values as pos_col

light_dark

Indicates whether pos_col, neg_col, and bg_col should be selected from light colors ("l"), dark colors ("d") or the full spectrum from light to dark ("f")

node_border_lwd

The thickness of the lines around the pie charts

layout_matrix

Users have the option of providing their own layout matrix for the network. This should be a two column matrix indicating the x and y coordinates of each node in the network.

zoom

Allows the user to zoom in and out on the image if the network is either running off the edges of the plot or too small in the middle of the plot.

xshift

A constant by which to shift the x values of all nodes in the network.

yshift

A constant by which to shift the y values of all nodes in the network.

node_radius

The size of the pie chart for each node.

label_nodes

A logical value indicating whether the nodes should be labeled. Users may want to remove labels for large networks.

label_offset

The amount by which to offset the node labels from the center of the nodes.

label_cex

The size of the node labels

legend_radius

The size of the legend indicating which pie piece corresponds to which traits.

legend_cex

The size of the labels in the legend.

legend_position

The position of the legend on the plot

arrow_offset

The distance from the center of the node to the arrow head.

arrow_length

The length of the head of the arrow

edge_lwd

The thickness of the arrows showing the interactions.

Details

For most networks, the default options will be fine, but there is a lot of room for modification if changes are desired

Value

This function invisibly returns a list of length two. The first element contains the igraph network object. The second contains the layout matrix for the network. This can be passed in as an argument ("layout_matrix") which provides more control to the user in the layout. Other network layouts from igraph can also be passed in here.

References

Csardi G, Nepusz T: The igraph software package for complex network research, InterJournal, Complex Systems 1695. 2006. https://igraph.org/