In meerapatelmd/chariotViz: Visualize the OMOP Vocabularies

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

chariotViz

Visualize the OMOP vocabularies from multiple dimensions using the DiagrammeR package.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("meerapatelmd/chariotViz")

Prerequisites

OMOP vocabularies loaded into a Postgres instance (see setupAthena).
R.cache R package that caches the query resultsets.

How It Works

S4 Classes

library(DiagrammeR)
DiagrammeR("
  sequenceDiagram;
    Postgres-->>omop.relationships: query; 
    omop.relationships->>nodes.and.edges: divide into;
    nodes.and.edges->>omop.graph: transform to
"
)

The raw OMOP data is fetched from the Postgres instance.

library(chariotViz)

omop_rels <- 
  fetch_omop_relationships(version_key = get_version_key())

The fetched data belongs to the omop.relationships S4 class.

class(omop_rels)

The omop.relationship class is converted to the nodes.and.edges S4 class.

omop_ne <- 
  create_nodes_and_edges(omop_relationships = omop_rels)

class(omop_ne)

From nodes.and.edges, an omop.graph S4 class object can be constructed.

omop_gr <- 
  construct_graph(omop_ne)

class(omop_gr)

The omop.graph can then be rendered, but due to its size, force must be set to TRUE in order to do so.

chariotViz(omop_gr)

Subsetting

An omop.relationships object can be subset using tidyverse-style filtering. Here, I am subsetting for all the relationships associated with Cancer Modifier. Since the node count is below the threshold set by default in the chariotViz function, the graph renders automatically and without having to set force to TRUE.

cancer_modifier_relationships <- 
  omop_rels %>% 
    filter_omop_relationships(
      vocabulary_id_1 == "Cancer Modifier")

cancer_modifier_ne <- 
  cancer_modifier_relationships %>% 
  create_nodes_and_edges()

cancer_modifier_graph <- 
  cancer_modifier_ne %>% 
  construct_graph()

chariotViz(cancer_modifier_graph)

Adding Pizzaz

The visualization is nice, but it needs a little oomph. A tooltip and visualization attributes can be added to the nodes.and.edges class object prior to graph construction. (Note that the tooltip is not rendering in this README, but view articles to see examples.)

DiagrammeR("
  sequenceDiagram;
    Postgres-->>omop.relationships: query; 
    omop.relationships->>nodes.and.edges: divide into;
    nodes.and.edges->>nodes.and.edges: add tooltip;
    nodes.and.edges->>omop.graph: transform to
"
)

cancer_modifier_relationships <- 
  omop_rels %>% 
    filter_omop_relationships(
      vocabulary_id_1 == "Cancer Modifier")

cancer_modifier_ne <- 
  cancer_modifier_relationships %>% 
  create_nodes_and_edges() %>% 
  add_tooltip()

cancer_modifier_graph <- 
  cancer_modifier_ne %>% 
  construct_graph()

chariotViz(cancer_modifier_graph)

In addition to the tooltip, the way the nodes and edges appear can also be customized.

DiagrammeR("
  sequenceDiagram;
    Postgres-->>omop.relationships: query; 
    omop.relationships->>nodes.and.edges: divide into;
    nodes.and.edges->>nodes.and.edges: add tooltip;
    nodes.and.edges->>nodes.and.edges: add attributes;
    nodes.and.edges->>omop.graph: transform to
"
)

cancer_modifier_relationships <- 
  omop_rels %>% 
    filter_omop_relationships(
      vocabulary_id_1 == "Cancer Modifier")

cancer_modifier_ne <- 
  cancer_modifier_relationships %>% 
  create_nodes_and_edges() %>% 
  add_tooltip() %>% 
  map_node_attributes() %>% 
  map_edge_attributes()

cancer_modifier_graph <- 
  cancer_modifier_ne %>% 
  construct_graph()

chariotViz(cancer_modifier_graph)

Resizing

Due to the large number of other relationships for Cancer Modifier, the height needs to be increased to make it more legible.

chariotViz(cancer_modifier_graph,
           height = 1500,
           width = 500)

Reconfiguring

The direction can also be reconfigured.

cancer_modifier_relationships <- 
  omop_rels %>% 
    filter_omop_relationships(
      vocabulary_id_1 == "Cancer Modifier")

cancer_modifier_ne <- 
  cancer_modifier_relationships %>% 
  create_nodes_and_edges() %>% 
  add_tooltip() %>% 
  map_node_attributes() %>% 
  map_edge_attributes()

cancer_modifier_graph <- 
  cancer_modifier_ne %>% 
  construct_graph(attr_theme = "tb")

chariotViz(cancer_modifier_graph,
           width = 2500,
           height = 500)

Adding Example Concepts

set.seed(seed = 1)
cancer_modifier_relationships <- 
  omop_rels %>% 
    filter_omop_relationships(
      vocabulary_id_1 == "Cancer Modifier")

cancer_modifier_ne <- 
  cancer_modifier_relationships %>% 
  create_nodes_and_edges() %>% 
  add_tooltip() %>% 
  map_node_attributes() %>% 
  map_edge_attributes()

cancer_modifier_graph <- 
  cancer_modifier_ne %>% 
  construct_graph() %>% 
  append_concept_examples(sample_size = 3)

chariotViz(cancer_modifier_graph)

chariotViz(cancer_modifier_graph,
           force = TRUE,
           height = 2500,
           width = 700)