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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 = "link_arc",
  node_size = 16,
  text_size = 3.88,
  label_size = text_size,
  text_col = "white",
  label_col = text_col,
  use_edges = TRUE,
  use_nodes = TRUE,
  use_stylized = FALSE,
  use_text = TRUE,
  use_labels = NULL,
  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    0.0589  0.0999 ->        x      0.993  0.763
#> 2 L1    0.0589  0.0999 ->        z      0.735 -0.826
#> 3 x     0.993   0.763  ->        y      1.67  -0.163
#> 4 y     1.67   -0.163  NA        NA    NA     NA    
#> 5 z     0.735  -0.826  ->        y      1.67  -0.163
#> #
#> # 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)