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interfaceplot

Source: R/interfaceplot.R
interfaceplot.Rd

Creates an interface plot of a modular model using qgraph and returns the interface information.

Usage

interfaceplot(
  x = ".",
  modules_to_include = NULL,
  modules_to_exclude = NULL,
  links_to_include = NULL,
  links_to_exclude = NULL,
  items_to_include = NULL,
  items_to_exclude = NULL,
  items_to_display = NULL,
  default_groups = list(default1 = list(name = "core", nodes = "core", color = "black",
    shape = "rectangle"), default2 = list(name = "modules", nodes = NULL, color =
    "#6c9ebf", shape = "ellipse")),
  highlight_groups = NULL,
  max_length_node_names = NULL,
  add_nodeName_legend = FALSE,
  max_num_edge_labels = NULL,
  max_num_nodes_for_edge_labels = 30,
  ...
)

Arguments

x

Either an interface list as returned by codeCheck or the path to the main folder of the model.

modules_to_include

NULL (default value) or a vector of strings with names of modules to include, e.g. c("core", "macro"). If NULL all modules are included.

modules_to_exclude

NULL (default value) or a vector of strings with names of modules to exclude, e.g. c("core"). If NULL no modules are excluded.

NULL (default value) or list of lists with attributes "to" and "from", that each take a vector of module names, e.g. list(list(to="macro", from="core")). If NULL all links are included.

NULL (default value) or list of lists with attributes "to" and "from", that each take a vector of module names, e.g. list(list(to="macro", from="core")). If NULL no links are excluded.

items_to_include

NULL (default value) or a vector of strings with names of items to include, e.g. c("vm_cesIO", "pm_pvp"). Regex patterns can also be passed, e.g. c("(v|p)m_.*"). If NULL all items are included.

items_to_exclude

NULL (default value) or a vector of strings with names of items to exclude, e.g. c("vm_cesIO", "pm_pvp"). Regex patterns can also be passed, e.g. c("sm_.*"). If NULL no items are excluded.

items_to_display

NULL (default value) or a vector of strings with names of items to display, e.g. c("vm_cesIO", "pm_pvp"). Regex patterns can also be passed, e.g. c(.m\ S+). If NULL no items are displayed.

default_groups

List of lists with default group definitions. Defines the default formatting of the interface plot. By default, there are two groups, see usage, a "core" group made up of only the "core" module and a "modules" group made up of all the rest. If a "core" module doesn't exist, then that group is simply ignored.

highlight_groups

NULL (default value) or a list of lists with highlight-group definitions. By defining highligh groups, additional/specalized formatting can be applied to select modules. A group is defined by a list with the following attributes:

  • name: a string with the group name. Will appear in legend.

  • nodes: a vector of strings with module names.

  • shape: a string with a valid qgraph shape.

  • color: a string with a valid qgraph color.

  • edges_to_highlight:

    • "all" = edges starting from and ending at the highlight group's nodes are colored

    • "incoming" = edges ending at the highlight group's nodes are colored

    • "outgoing" = edges starting from the highlight group's nodes are colored

    • "within" = only edges that departed from the highlight group's nodes and end at them as well are colored

  • edges_to_ignore:

    • "outside" edges that neither start from or end at any of the group's nodes are ignored

    • "incoming" edges that do not depart from one of the group's nodes are ignored

    • "outgoing" edges that do not arrive at one of the group's nodes are ignored

    • "outgoing_to_no_return" edges that departing from nodes outside of the group and not ending at nodes within the group are ignored

An example: list(list(name = "highlight", nodes = "welfare", color = "#ff8f00", shape = "ellipse", edges_to_highlight = "outgoing", edges_to_ignore = "outside")).

max_length_node_names

NULL (default value) or an integer n giving the maximum number of characters allowed in the node names. If not NULL, node names are truncated after n characters, e.g. n=3: "example" -> "exa.".

add_nodeName_legend

Logical (default FALSE) to add node names in legend, structured by group.

max_num_edge_labels

NULL (default value), an integer or the string "adjust". If NULL, all edge lables are displayed. If given an integer n, a maximum of n edge labels are shown. If set to "adjust", the number of edge labels displayed decreases with the number of nodes.

max_num_nodes_for_edge_labels

Integer, (default value = 30). The maximum number of nodes after which no edge labels are displayed.

...

Optional arguments to qgraph.

Value

A tibble with the edge list and interface items.

Details

What modules (=nodes), links (=edges) and items (=what is passed along the edges) are taken into account when creating the plot can be fine-tuned with the "_include", "_exclude" arguments.

The "default"- and "highlight_groups" arguments control the formatting (and also the composition through "highlight_group$edges_to_ignore"). Groups in qqgraph are a way of clustering nodes together. The default formatting of the plot is defined with the "default_groups" argument. On top of that additional groups can be defined with the "highlight_groups" argument.

The rest of the arguments are pretty self-explanatory. Just remember that qgraph arguments can be passed on as well! Useful ones include: fade=T/F, legend=T/F, legend.cex (size of the legend font), GLratio (graph/legend size ratio, edge.label.cex (size of the edge label font)).

See also

codeCheck,qgraph

Author

Johannes Koch