plot_dag: Plot DAG

Description

Creates a ggplot from a dagitty object, using packages dagitty and ggdag. Mimics format and colors used on the dagitty homepage https://www.dagitty.net. Please note the recommendation in argument label_shift below: Getting the values for label_shift right can be an iterative and slightly tedious procedure. It is highly recommended to evaluate the result of the current values already in the saved plot using, e.g., ggsave and not in the RStudio Viewer.

Usage

plot_dag(
  dag,
  node_outc = NULL,
  node_expo = NULL,
  node_adj = NULL,
  node_latent = NULL,
  path_causal = NULL,
  path_biased = NULL,
  label = NULL,
  label_shift = NULL,
  label_size = 2.5,
  node_size = 7,
  node_stroke = 1,
  e_w = 0.4,
  cap_mm = 4,
  scc = FALSE,
  scc_size = c(0.1, 0.35),
  scc_shift = c(0, 0),
  scc_angle = 0
)

Value

A ggplot object.

Arguments

dag: An object of class dagitty. Can be created by using dagitty::dagitty('[model_code]') or scc_to_dag(). If your DAG has been created by scc_to_dag(), make sure to pass only the first element (named dag) to plot_dag.
node_outc: A single element of type character or NULL (default). If the outcome has not yet been specified in dag, it can be done here by specifiying the name of the corresponding node.
node_expo: A single element of type character or NULL (default). If the exposure has not yet been specified in dag, it can be done here by specifiying the name of the corresponding node.
node_adj: A character vector or NULL (default). Specify the names of nodes that should be defined as "adjusted".
node_latent: A character vector or NULL (default). Specify the names of nodes that should be defined as "latent".
path_causal: A character vector or NULL (default). Specify the names of the paths in format "V1->V2" that should be defined as "causal".
path_biased: A character vector or NULL (default). Specify the names of the paths in format "V1->V2" that should be defined as "biased".
label: A named character vector or NULL (default). Change the name of nodes in the graph, i.e., labels. The vector elements correspond to the new names, the vector names correspond to the old node names, i.e., label = c(old_name = "new_name").
label_shift: A named list (with all elements being numerical vectors of length 2) or NULL (default). Numerical values are used to move the labels of the corresponding nodes in x and y direction, respectively. The list names correspond to the nodes to which the values apply. Possible list names are the node names (initial names prior to changing them via label), node types, i.e., outcome, exposure, adjusted, latent, and other, as well as all, which applies to all nodes. If a node is addressed by several entries, e.g., its name and all, all entries are summed up. See the example below. Getting the values for label_shift right can be an iterative and slightly tedious procedure. It is highly recommended to evaluate the result of the current values already in the saved plot using, e.g., ggsave and not in the RStudio Viewer.
label_size: A single numeric value, which controls the font size of the label. Default is 2.5.
node_size: A single numeric value, which controls the size of the circle that represents the node. Default is 7.
node_stroke: A single numeric value, which controls the size of the black border around the node circles. Default is 1.
e_w: A single numeric value, which controls edge width. Default is 0.4.
cap_mm: A single numeric value, which controls the distance, i.e., white space, between when the node ends and the edge begins/ the edge ends and the node begins. Higher values correspond to shorter edges/arrows. Default is 4.
scc: TRUE or FALSE (default). Only applies to DAGs that are based on sufficient-component cause (SCC) models. If TRUE, an ellipse is added to the DAG, which should surround all sufficient cause variables, if they are a determinative set of sufficient causes, as suggested by VanderWeele and Robins (2007). If the DAG is not based on a SCC, leave scc at FALSE.
scc_size: A numeric vector of length 2, which controls the size of the ellipse. Default is c(0.1, 0.35).
scc_shift: A numeric vector of length 2, which controls the shift of the complete ellipse in x and y direction. Default is c(0, 0).
scc_angle: A single numeric value, which controls rotiation of the ellipse in degree units. Default is 0.

References

VanderWeele TJ, Robins JM (2007): Directed acyclic graphs, sufficient causes, and the properties of conditioning on a common effect. American Journal of Epidemiology 166 (9): 1096–1104.

Examples

Run this code

if (FALSE) { # rlang::is_installed(c("ggdag", "ggforce", "ggraph"))
# Transform SCC model into a DAG
dag <- scc_to_dag(scc_rain)[["dag"]]

# Plot DAG
plot_dag(dag, label_shift = list(all = c(0,0.15), outcome = c(0.05,0)))

# plot_dag() works also with dagitty objects created in other ways
dag_to_plot <- dagitty::dagitty('dag {
bb="-2.628,-2.412,2.659,2.378"
V1 [pos="-2.128,-1.912"]
V2 [pos="-0.031,0.035"]
V3 [pos="2.159,1.878"]
V1 -> V2
V2 -> V3
}')
plot_dag(dag_to_plot, node_outc = "V3", node_expo = "V1", label = c(V3 = "outcome"))
}