In meerapatelmd/chariotViz: Visualize the OMOP Vocabularies

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  error   = FALSE,
  cache.path = file.path(R.cache::getCachePath(),
                         "chariotViz",
                         "vignettes")
)

library(chariot)
genomic_vocabularies <- 
queryAthena("SELECT vocabulary_id,COUNT(*) FROM omop_vocabulary.concept WHERE LOWER(concept_class_id) LIKE '%variant%' GROUP BY vocabulary_id;")
genomic_vocabularies

Last Update On: r as.character(Sys.time())

library(chariotViz)
version_key <- 
  get_version_key()

rmd_print_version(version_key, 
                  !!!genomic_vocabularies$vocabulary_id)

The following vocabularies related to genomics concepts are identified.

library(chariot)
genomic_vocabularies <- 
queryAthena("SELECT vocabulary_id,COUNT(*) FROM omop_vocabulary.concept WHERE LOWER(concept_class_id) LIKE '%variant%' GROUP BY vocabulary_id;")
genomic_vocabularies

An omop.relationships S4 class object is fetched for these vocabularies.

library(chariotViz)

omop_relationships <- 
  fetch_omop_relationships(
    !!!genomic_vocabularies$vocabulary_id,
    version_key = get_version_key())

omop_nodes_and_edges <- 
  create_nodes_and_edges(omop_relationships = omop_relationships)

omop_nodes_and_edges <- 
  omop_nodes_and_edges %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_nodes_and_edges)

chariotViz(
  omop_graph = omop_graph,
  force = TRUE, 
  width = 1500,
  height = 2000
)

After remapping fillcolor by domain, it is evident that some of these vocabularies cross multiple domains, specifically Condition and Observation.

omop_graph <- 
  remap_fillcolor_by_domain(omop_graph = omop_graph)
chariotViz(
  omop_graph = omop_graph,
  force = TRUE, 
  width = 1500,
  height = 2000
)

A filter is applied for Measurement domains only.

omop_relationships <- 
omop_relationships %>% 
  filter_omop_relationships(
    domain_id_1 == "Measurement",
    domain_id_2 == "Measurement"
  )
omop_nodes_and_edges <- 
  create_nodes_and_edges(omop_relationships = omop_relationships)

omop_nodes_and_edges <- 
  omop_nodes_and_edges %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_nodes_and_edges)

chariotViz(
  omop_graph = omop_graph,
  force = TRUE, 
  width = 1500,
  height = 2000
)

The relationships are subset based on whether they are lateral, taxonomical, or mapping.

Mapping Relationships

omop_relationships_mapping <- 
omop_relationships %>% 
  filter_for_mapping_relationships() %>% 
  # Filtered out because it is a bad data capture using the regex for all variant concept classes
  filter_omop_relationships(concept_class_id_1 != "Lab Test")

omop_nodes_and_edges_mapping <- 
  create_nodes_and_edges(omop_relationships_mapping)

omop_nodes_and_edges_mapping <- 
  omop_nodes_and_edges_mapping %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_nodes_and_edges_mapping)

chariotViz(
  omop_graph = omop_graph,
  height = 1000
)

The Maps to relationship is isolated to see how Variants represented in normal vocabularies are normalized to the OMOP Extension.

omop_relationships_mapping <- 
omop_relationships_mapping %>% 
  filter_for_mapping_relationships() %>% 
  # Filtered out because it is a bad data capture using the regex for all variant concept classes
  filter_omop_relationships(relationship_id == "Maps to")

omop_nodes_and_edges_mapping <- 
  create_nodes_and_edges(omop_relationships_mapping)

omop_nodes_and_edges_mapping <- 
  omop_nodes_and_edges_mapping %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_nodes_and_edges_mapping)

chariotViz(
  omop_graph = omop_graph,
  height = 1000
)

Example concepts are added for each node.

omop_graph <- 
  omop_graph %>% 
  append_concept_examples(sample_size = 3)

chariotViz(
  omop_graph = omop_graph,
  force = TRUE
)

Taxonomical Relationships

omop_relationships_taxonomy <- 
omop_relationships %>% 
  filter_for_taxonomy_relationships() %>% 
  # Filtered out because it is a bad data capture using the regex for all variant concept classes
  filter_omop_relationships(concept_class_id_1 != "Lab Test")

omop_nodes_and_edges_taxonomy <- 
  create_nodes_and_edges(omop_relationships_taxonomy)

omop_nodes_and_edges_taxonomy <- 
  omop_nodes_and_edges_taxonomy %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_nodes_and_edges_taxonomy) 

chariotViz(
  omop_graph = omop_graph,
  height = 400,
  width = 400
)

omop_graph <- 
  append_concept_examples(omop_graph)

chariotViz(
  omop_graph = omop_graph,
  height = 600,
  width = 1000
)

Lateral Relationships

omop_relationships_lateral <- 
omop_relationships %>% 
  filter_for_lateral_relationships() %>% 
  # Filtered out because it is a bad data capture using the regex for all variant concept classes
  filter_omop_relationships(concept_class_id_1 != "Precoordinated pair",
                            vocabulary_id_1 != "NCIt")

omop_nodes_and_edges_lateral <- 
  create_nodes_and_edges(omop_relationships_lateral)

omop_nodes_and_edges_lateral <- 
  omop_nodes_and_edges_lateral %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes() 

omop_graph <- 
  construct_graph(omop_nodes_and_edges_lateral,
                  attr_theme = "lr") %>% 
  remap_fillcolor_by_concept_class(fillcolor_map = c(`Transcript Variant` = "cadetblue",
                                                     `Protein Variant` = "indianred",
                                                     `Genomic Variant` = "mediumpurple"))

chariotViz(
  omop_graph = omop_graph,
  height = 500,
  width = 500
)

omop_graph <- 
  append_concept_examples(omop_graph)

chariotViz(
  omop_graph = omop_graph,
  height = 300,
  width = 1000
)

HGNC

omop_relationships_hgnc <- 
  fetch_omop_relationships("HGNC",
                           version_key = get_version_key()) %>% 
  filter_omop_relationships(
                            vocabulary_id_1 == "HGNC")

omop_nodes_and_edges_hgnc <- 
  create_nodes_and_edges(omop_relationships_hgnc)

omop_nodes_and_edges_hgnc <- 
  omop_nodes_and_edges_hgnc %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes() 

omop_graph <- 
  construct_graph(omop_nodes_and_edges_hgnc,
                  attr_theme = "lr")
chariotViz(
  omop_graph = omop_graph,
  height = 500,
  width = 500
)

OMOP Extension

omop_relationships_oe <- 
  fetch_omop_relationships("OMOP Extension",
                           version_key = get_version_key()) %>% 
  filter_omop_relationships(
                            vocabulary_id_1 == "OMOP Extension",
                            concept_class_id_1 %in% c("Protein Variant",
                                                      "Genomic Variant",
                                                      "Transcript Variant"))

omop_nodes_and_edges_oe <- 
  create_nodes_and_edges(omop_relationships_oe)

omop_nodes_and_edges_oe <- 
  omop_nodes_and_edges_oe %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes() 

omop_graph <- 
  construct_graph(omop_nodes_and_edges_oe,
                  attr_theme = "lr")

chariotViz(
  omop_graph = omop_graph,
  height = 1500,
  width = 1500
)

chariotViz(
  omop_graph = omop_graph %>% 
                remap_fillcolor_by_domain(),
  height = 1000,
  width = 1500
)

omop_relationships_oe <- 
  fetch_omop_relationships("OMOP Extension",
                           version_key = get_version_key()) %>% 
  filter_omop_relationships(
                            vocabulary_id_1 == "OMOP Extension",
                            concept_class_id_1 %in% c("Protein Variant",
                                                      "Genomic Variant",
                                                      "Transcript Variant"),
                            domain_id_1 == "Measurement",
                            domain_id_1 != domain_id_2)

omop_nodes_and_edges_oe <- 
  create_nodes_and_edges(omop_relationships_oe)

omop_nodes_and_edges_oe <- 
  omop_nodes_and_edges_oe %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes() 

omop_graph <- 
  construct_graph(omop_nodes_and_edges_oe,
                  attr_theme = "lr")

chariotViz(
  omop_graph = omop_graph,
  height = 500,
  width = 500
)

omop_relationships_oe <- 
  fetch_omop_relationships("OMOP Extension",
                           version_key = get_version_key()) %>% 
  filter_omop_relationships(
                            vocabulary_id_1 == "OMOP Extension",
                            concept_class_id_1 %in% c(#"Protein Variant",
                                                      #"Genomic Variant",
                                                      "Transcript Variant"),
                            domain_id_1 == "Measurement",
                            domain_id_1 == domain_id_2)

omop_nodes_and_edges_oe <- 
  create_nodes_and_edges(omop_relationships_oe)

omop_nodes_and_edges_oe <- 
  omop_nodes_and_edges_oe %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes() 

omop_graph <- 
  construct_graph(omop_nodes_and_edges_oe,
                  attr_theme = "lr")

chariotViz(
  omop_graph = omop_graph,
  height = 1500,
  width = 1500
)

omop_relationships_oe <- 
  fetch_omop_relationships("OMOP Extension",
                           version_key = get_version_key()) %>% 
  filter_out_mapping_relationships() %>%
  filter_omop_relationships(
                            vocabulary_id_1 == "OMOP Extension",
                            concept_class_id_1 %in% c(#"Protein Variant",
                                                      #"Genomic Variant",
                                                      "Transcript Variant"),
                            domain_id_1 == "Measurement",
                            domain_id_1 == domain_id_2)

omop_nodes_and_edges_oe <- 
  create_nodes_and_edges(omop_relationships_oe)

omop_nodes_and_edges_oe <- 
  omop_nodes_and_edges_oe %>% 
  add_tooltip() %>%
  map_node_attributes() %>% 
  map_edge_attributes() 

omop_graph <- 
  construct_graph(omop_nodes_and_edges_oe,
                  attr_theme = "lr")

chariotViz(
  omop_graph = omop_graph,
  height = 500,
  width = 500
)