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Canonicalize a DAG

Source: R/canonical.R
canonicalize.Rd

Takes an input graph with bidirected edges and replaces every bidirected edge x <-> y with a substructure x <- L -> y, where L is a latent variable. See dagitty::canonicalize() for details. Undirected edges are not currently supported in ggdag.

Usage

node_canonical(.dag, ...)

ggdag_canonical(
  .tdy_dag,
  ...,
  edge_type = ggdag_option("edge_type", "link_arc"),
  node_size = ggdag_option("node_size", 16),
  text_size = ggdag_option("text_size", 3.88),
  label_size = ggdag_option("label_size", text_size),
  text_col = ggdag_option("text_col", "white"),
  label_col = ggdag_option("label_col", text_col),
  use_edges = ggdag_option("use_edges", TRUE),
  use_nodes = ggdag_option("use_nodes", TRUE),
  use_stylized = ggdag_option("use_stylized", FALSE),
  use_text = ggdag_option("use_text", TRUE),
  use_labels = ggdag_option("use_labels", NULL),
  label_geom = ggdag_option("label_geom", geom_dag_label_repel),
  label = NULL,
  text = NULL,
  node = deprecated(),
  stylized = deprecated()
)

Arguments

.dag, .tdy_dag

input graph, an object of class tidy_dagitty or dagitty

...

additional arguments passed to tidy_dagitty()

edge_type

The type of edge, one of "link_arc", "link", "arc", "diagonal".

node_size

The size of the nodes.

text_size

The size of the text.

label_size

The size of the labels.

text_col

The color of the text.

label_col

The color of the labels.

use_edges

A logical value. Include a geom_dag_edges*() function? If TRUE, which is determined by edge_type.

use_nodes

A logical value. Include geom_dag_point()?

use_stylized

A logical value. Include geom_dag_node()?

use_text

A logical value. Include geom_dag_text()?

use_labels

A logical value. Include a label geom? The specific geom used is controlled by label_geom.

label_geom

A geom function to use for drawing labels when use_labels = TRUE. Default is geom_dag_label_repel. Other options include geom_dag_label, geom_dag_text_repel, geom_dag_label_repel2, and geom_dag_text_repel2.

label

The bare name of a column to use for labels. If use_labels = TRUE, the default is to use label.

text

The bare name of a column to use for geom_dag_text(). If use_text = TRUE, the default is to use name.

node

Deprecated.

stylized

Deprecated.

Value

a tidy_dagitty that includes L or a ggplot

Examples

dag <- dagify(y ~ x + z, x ~ ~z)

ggdag(dag)


node_canonical(dag)
#> # DAG:
#> # A `dagitty` DAG with: 4 nodes and 4 edges
#> # Latent Variable: L1
#> #
#> # Data:
#> # A tibble: 5 × 7
#>   name          x             y direction to         xend          yend
#>   <chr>     <dbl>         <dbl> <fct>     <chr>     <dbl>         <dbl>
#> 1 L1    -0.000782  0.803        ->        x     -0.817     0.0000000178
#> 2 L1    -0.000782  0.803        ->        z      0.818    -0.0000000183
#> 3 x     -0.817     0.0000000178 ->        y     -0.000782 -0.803       
#> 4 y     -0.000782 -0.803        NA        NA    NA        NA           
#> 5 z      0.818    -0.0000000183 ->        y     -0.000782 -0.803       
#> #
#> # ℹ Use `pull_dag() (`?pull_dag`)` to retrieve the DAG object and `pull_dag_data() (`?pull_dag_data`)` for the data frame
ggdag_canonical(dag)