README.md

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With the DiagrammeR package you can create, modify, analyze, and visualize network graph diagrams. The output can be incorporated into RMarkdown documents, integrated with Shiny web apps, converted to other graph formats, or exported as PNG, PDF, or SVG files.

It's possible to make the above graph diagram using a combination of DiagrammeR functions strung together with the magrittr %>% pipe:

library(DiagrammeR)

create_random_graph(
  n = 140, m = 100,
  directed = FALSE,
  set_seed = 23) %>%
  join_node_attrs(
    df = get_s_connected_cmpts(.)) %>%
  join_node_attrs(
    df = get_degree_total(.)) %>%
  colorize_node_attrs(
    node_attr_from = sc_component,
    node_attr_to = fillcolor,
    alpha = 80) %>%
  rescale_node_attrs(
    node_attr_from = total_degree,
    to_lower_bound = 0.2,
    to_upper_bound = 1.5,
      node_attr_to = height) %>%
  select_nodes_by_id(
    nodes = get_articulation_points(.)) %>%
  set_node_attrs_ws(
    node_attr = peripheries,
    value = 2) %>%
  set_node_attrs_ws(
    node_attr = penwidth,
    value = 3) %>%
  clear_selection() %>%
  set_node_attr_to_display(
    attr = NULL) %>%
  render_graph()

DiagrammeR's graph functions allow you to create graph objects, modify those graphs, get information from the graphs, create a series of graphs, and do many other useful things.

This functionality makes it possible to generate a network graph with data available in tabular datasets. Two specialized data frames contain node data and attributes (node data frames) and edges with associated edge attributes (edge data frames). Because the attributes are always kept alongside the node and edge definitions (within the graph object itself), we can easily work with them and specify styling attributes to differentiate nodes and edges by size, color, shape, opacity, length, and more.

A Network Graph Example

Let's create a property graph that pertains to contributors to three software projects. This graph has nodes representing people and projects. The attributes name, age, join_date, email, follower_count, following_count, and starred_count are specific to the person nodes while the project, start_date, stars, and language attributes apply to the project nodes. The edges represent the relationships between the people and the project.

The example graph file repository.dgr is available in the extdata/example_graphs_dgr/ directory in the DiagrammeR package (currently, only for the Github version). We can load it into memory by using the open_graph() function, with system.file() to provide the location of the file within the package.

library(DiagrammeR)

# Load in a the small repository graph
graph <-
  open_graph(
    system.file(
      "extdata/example_graphs_dgr/repository.dgr",
      package = "DiagrammeR"))

We can always view the property graph with the render_graph() function.

render_graph(graph, layout = "kk")

Now that the graph is set up, you can create queries with magrittr pipelines to get specific answers from the graph.

Get the average age of all the contributors. Select all nodes of type person (not project). Each node of that type has non-NA age attribute, so, get that attribute as a vector with get_node_attrs_ws() and then calculate the mean with R's mean() function.

graph %>% 
  select_nodes(
    conditions = type == "person") %>%
  get_node_attrs_ws(
    node_attr = age) %>%
  mean()
#> [1] 33.6

We can get the total number of commits to all projects. We know that all edges contain the numerical commits attribute, so, select all edges (select_edges() by itself selects all edges in the graph). After that, get a numeric vector of commits values and then get its sum() (all commits to all projects).

graph %>% 
  select_edges() %>%
  get_edge_attrs_ws(
    edge_attr = commits) %>%
  sum()
#> [1] 5182

Single out the one known as Josh and get his total number of commits as a maintainer and as a contributor. Start by selecting the Josh node with select_nodes(conditions = name == "Josh"). In this graph, we know that all people have an edge to a project and that edge can be of the relationship (rel) type of contributor or maintainer. We can migrate our selection from nodes to outbound edges with trav_out_edges() (and we won't provide a condition, just all the outgoing edges from Josh will be selected). Now we have a selection of 2 edges. Get that vector of commits values with get_edge_attrs_ws() and then calculate the sum(). This is the total number of commits.

graph %>% 
  select_nodes(
    conditions = name == "Josh") %>%
  trav_out_edge() %>%
  get_edge_attrs_ws(
    edge_attr = commits) %>%
  sum()
#> [1] 227

Get the total number of commits from Louisa, just from the maintainer role though. In this case we'll supply a condition in trav_out_edge(). This acts as a filter for the traversal and this means that the selection will be applied to only those edges where the condition is met. Although there is only a single value, we'll still use sum() after get_edge_attrs_ws() (a good practice because we may not know the vector length, especially in big graphs).

graph %>% 
  select_nodes(
    conditions = name == "Louisa") %>%
  trav_out_edge(
    conditions = rel == "maintainer") %>%
  get_edge_attrs_ws(
    edge_attr = commits) %>%
  sum()
#> [1] 236

How do we do something more complex, like, get the names of people in graph above age 32? First, select all person nodes with select_nodes(conditions = type == "person"). Then, follow up with another select_nodes() call specifying age > 32. Importantly, have set_op = "intersect" (giving us the intersection of both selections).

Now that we have the starting selection of nodes we want, we need to get all values of these nodes' name attribute as a character vector. We do this with the get_node_attrs_ws() function. After getting that vector, sort the names alphabetically with the R function sort(). Because we get a named vector, we can use unname() to not show us the names of each vector component.

graph %>% 
  select_nodes(
    conditions = type == "person") %>%
  select_nodes(
    conditions = age > 32,
    set_op = "intersect") %>%
  get_node_attrs_ws(
    node_attr = name) %>%
  sort() %>%
  unname()
#> [1] "Jack"   "Jon"    "Kim"    "Roger"  "Sheryl"

That supercalc project is progressing quite nicely. Let's get the total number of commits from all people to that most interesting project. Start by selecting that project's node and work backwards. Traverse to the edges leading to it with trav_in_edge(). Those edges are from committers and they all contain the commits attribute with numerical values. Get a vector of commits and then get the sum (there are 1676 commits).

graph %>% 
  select_nodes(
    conditions = project == "supercalc") %>%
  trav_in_edge() %>%
  get_edge_attrs_ws(
    edge_attr = commits) %>%
  sum()
#> [1] 1676

Kim is now a contributor to the stringbuildeR project and has made 15 new commits to that project. We can modify the graph to reflect this.

First, add an edge with add_edge(). Note that add_edge() usually relies on node IDs in from and to when creating the new edge. This is almost always inconvenient so we can instead use node labels (we know they are unique in this graph) to compose the edge, setting use_labels = TRUE.

The rel value in add_edge() was set to contributor -- in a property graph we always have values set for all node type and edge rel attributes. We will set another attribute for this edge (commits) by first selecting the edge (it was the last edge made, so we can use select_last_edges_created()), then, use set_edge_attrs_ws() and provide the attribute/value pair. Finally, clear the active selections with clear_selection(). The graph is now changed, have a look.

graph <- 
  graph %>%
  add_edge(
    from = "Kim",
    to = "stringbuildeR",
    rel = "contributor") %>%
  select_last_edges_created() %>%
  set_edge_attrs_ws(
    edge_attr = commits,
    value = 15) %>%
  clear_selection()

render_graph(graph, layout = "kk")

Get all email addresses for contributors (but not maintainers) of the randomizer and supercalc88 projects. With trav_in_edge() we just want the contributer edges/commits. Once on those edges, hop back unconditionally to the people from which the edges originate with trav_out_node(). Get the email values from those selected individuals as a sorted character vector.

graph %>% 
  select_nodes(
    conditions = 
      project == "randomizer" | 
      project == "supercalc") %>%
  trav_in_edge(
    conditions = rel == "contributor") %>%
  trav_out_node() %>%
  get_node_attrs_ws(
    node_attr = email) %>%
  sort() %>%
  unname()
#> [1] "[email protected]"      "[email protected]"     
#> [3] "[email protected]"      "[email protected]-fun.com"   
#> [5] "[email protected]" "[email protected]-q-w-o.net"  
#> [7] "[email protected]" 

Which people have committed to more than one project? This is a matter of node degree. We know that people have edges outward and projects and edges inward. Thus, anybody having an outdegree (number of edges outward) greater than 1 has committed to more than one project. Globally, select nodes with that condition using select_nodes_by_degree("outdeg > 1"). Once getting the name attribute values from that node selection, we can provide a sorted character vector of names.

graph %>%
  select_nodes_by_degree(
    expressions = "outdeg > 1") %>%
  get_node_attrs_ws(
    node_attr = name) %>%
  sort() %>%
  unname()
#> [1] "Josh"   "Kim"    "Louisa"

Installation

DiagrammeR is used in an R environment. If you don't have an R installation, it can be obtained from the Comprehensive R Archive Network (CRAN).

You can install the development version of DiagrammeR from GitHub using the devtools package.

devtools::install_github("rich-iannone/DiagrammeR")

Or, get it from CRAN.

install.packages("DiagrammeR")

If you encounter a bug, have usage questions, or want to share ideas to make this package better, feel free to file an issue.

Code of Conduct

Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

License

MIT © Richard Iannone



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DiagrammeR documentation built on Sept. 7, 2017, 1:06 a.m.