use DiagrammeR

Author: grlloyd

DESCRIPTION

@@ -72,5 +72,5 @@ Suggests:
 VignetteBuilder: knitr
 Imports: methods,ontologyIndex,
     datasets, graphics, stats, utils, knitr, 
-    SummarizedExperiment, S4Vectors, rols, igraph
+    SummarizedExperiment, S4Vectors, rols, igraph, DiagrammeR
 biocViews: WorkflowStep

NAMESPACE

@@ -8,6 +8,7 @@ S3method(.DollarNames,iterator)
 S3method(.DollarNames,metric)
 S3method(.DollarNames,model)
 S3method(.DollarNames,model_dag)
+S3method(.DollarNames,model_dag_chart)
 S3method(.DollarNames,model_node)
 S3method(.DollarNames,optimiser)
 S3method(.DollarNames,prediction_node)
@@ -44,6 +45,7 @@ export(entity_stato)
 export(enum)
 export(enum_stato)
 export(example_chart)
+export(example_dag)
 export(example_iterator)
 export(example_model)
 export(get_description)
@@ -169,17 +171,18 @@ exportMethods(stato_id)
 exportMethods(stato_name)
 exportMethods(stato_summary)
 exportMethods(value)
+import(DiagrammeR)
 import(S4Vectors)
 import(SummarizedExperiment)
 import(datasets)
-import(ggplot2)
 import(methods)
+importFrom(DiagrammeR,add_edge)
+importFrom(DiagrammeR,add_node)
+importFrom(DiagrammeR,create_graph)
+importFrom(DiagrammeR,render_graph)
+importFrom(DiagrammeR,set_edge_attrs)
+importFrom(DiagrammeR,set_node_attrs)
 importFrom(graphics,plot)
-importFrom(igraph,graph_from_data_frame)
-importFrom(igraph,layout_as_tree)
-importFrom(igraph,layout_in_circle)
-importFrom(igraph,layout_randomly)
-importFrom(igraph,layout_with_sugiyama)
 importFrom(knitr,purl)
 importFrom(ontologyIndex,get_ontology)
 importFrom(stats,runif)

R/chart_node_class.R

@@ -40,7 +40,8 @@ chart_node = function(name = character(0), description = character(0), chart = N
     ),
     prototype = list(
         chart = NULL,
-        input_objects = list()
+        input_objects = list(),
+        .params=c('chart','input_objects')
     )
 )
 
@@ -109,4 +110,4 @@ setMethod(f = "show",
 
 #' @export
 #' @rdname autocompletion
-setMethod('.DollarNames','chart_node',.DollarNames.chart_node) 
+setMethod('.DollarNames','chart_node',.DollarNames.chart_node)

R/data_node_class.R

@@ -36,7 +36,7 @@ data_node = function(name = character(0), description = character(0), data = NUL
     ),
     prototype = list(
         data = NULL,
-        input_data = NULL
+        .params=c('data','input_data')
     )
 )
 
@@ -100,4 +100,4 @@ setMethod(f = "show",
 
 #' @export
 #' @rdname autocompletion
-setMethod('.DollarNames','data_node',.DollarNames.data_node) 
+setMethod('.DollarNames','data_node',.DollarNames.data_node)

R/example_objects.R

@@ -201,13 +201,39 @@ chart_node_example = function() {
     return(NULL)
 }
 
-
-
-
-
-
-
-
-
-
-
+#' Example DAG
+#'
+#' An example model_dag for testing the DAG chart functionality.
+#' Creates a simple DAG with two connected nodes.
+#' @export
+#' @return model_dag object
+#' @examples
+#' DAG = example_dag()
+#' C = model_dag_chart()
+#' chart_plot(C, DAG)
+example_dag = function() {
+    # Create example nodes
+    node1 = example_model(value_1 = 5, value_2 = 10)
+    node2 = example_model(value_1 = 15, value_2 = 25)
+    
+    # Create edges
+    edges = list(
+        list(from = "node1", to = "node2")
+    )
+    
+    # Create nodes list
+    nodes = list(
+        node1 = node1,
+        node2 = node2
+    )
+    
+    # Create the DAG
+    dag = model_dag(
+        name = "Example DAG",
+        description = "A simple example DAG with two connected nodes",
+        edges = edges,
+        nodes = nodes
+    )
+    
+    return(dag)
+}