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")
)

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

library(chariotViz)
version_key <- 
  get_version_key()

rmd_print_version(version_key, 
                  "RxNorm")

library(chariotViz)
library(tidyverse)

omop_relationships <- 
  fetch_omop_relationships(
    version_key = get_version_key())

omop_relationships_a <- 
omop_relationships %>% 
  filter_omop_relationships(domain_id_1 != domain_id_2)


omop_ne_a <- 
  create_nodes_and_edges(omop_relationships_a) %>% 
  add_tooltip() %>% 
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_ne_a)

chariotViz(omop_graph = omop_graph)

omop_relationships_ucum <- 
  omop_relationships_a %>% 
  filter_omop_relationships(vocabulary_id_1 == 'UCUM'|vocabulary_id_2 == 'UCUM')
omop_ne_ucum <- 
  create_nodes_and_edges(omop_relationships_ucum) %>% 
  add_tooltip() %>% 
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_ne_ucum) %>% 
  remap_fillcolor_by_domain()

chariotViz(omop_graph = omop_graph)

construct_node_legend(omop_graph)
construct_edge_legend(omop_graph)

omop_relationships_icdo3 <- 
  omop_relationships_a %>% 
  filter_omop_relationships(vocabulary_id_1 == 'ICDO3')
omop_ne_icdo3 <- 
  create_nodes_and_edges(omop_relationships_icdo3) %>% 
  add_tooltip() %>% 
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_ne_icdo3) %>% 
  remap_fillcolor_by_domain()

chariotViz(omop_graph = omop_graph)

construct_node_legend(omop_graph)
construct_edge_legend(omop_graph)

omop_relationships_naaccr <- 
  omop_relationships_a %>% 
  filter_omop_relationships(vocabulary_id_1 == 'NAACCR')
omop_ne_naaccr <- 
  create_nodes_and_edges(omop_relationships_naaccr) %>% 
  add_tooltip() %>% 
  map_node_attributes() %>% 
  map_edge_attributes()

omop_graph <- 
  construct_graph(omop_ne_naaccr) %>% 
  remap_fillcolor_by_domain() 

chariotViz(omop_graph = omop_graph)

construct_node_legend(omop_graph)
construct_edge_legend(omop_graph)