R/omop_color_maps.R

In mpatel-cai/chariot2: What the Package Does (One Line, Title Case)

rxnorm_class_colors <- 
  list(
    `Branded Drug` = 'springgreen3',
    `Clinical Drug` = 'springgreen3',
    `Branded Pack` = 'orange2',
    `Clinical Pack` = 'orange2',
    `Quant Branded Drug` = 'royalblue2',
    `Quant Clinical Drug` = 'royalblue2',
    `Brand Name` = 'violetred2',
    `Branded Drug Comp` = 'peachpuff2',
    `Clinical Drug Comp` = 'peachpuff2',
    `Ingredient` = 'violetred2',
    `Multiple Ingredients` = 'violetred2',
    `Clinical Dose Group` = 'lightpink2',
    `Dose Form Group` = 'lightpink2',
    `Branded Dose Group` = 'lightpink2',
    `Precise Ingredient` = 'violetred2',
    `Clinical Drug Form` = 'purple2',
    `Dose Form` = 'purple2',
    `Branded Drug Form` = 'purple2',
    `Branded Drug Box` = 'lightgoldenrod2',
    `Clinical Drug Box` = 'lightgoldenrod2',
    `Branded Pack Box` = 'lightgoldenrod2',
    `Clinical Pack Box` = 'lightgoldenrod2',
    `Quant Branded Box` = 'lightgoldenrod2',
    `Quant Clinical Box` = 'lightgoldenrod2',
    `Marketed Product` = 'lightgoldenrod2')

rxnorm_concept_class_color_groups <-
  c('Branded Drug' = 'Green colors',
    'Clinical Drug' = 'Green colors',
    'Branded Pack' = 'Orange colors',
    'Clinical Pack' = 'Orange colors',
    'Quant Branded Drug' = 'Blue colors',
    'Quant Clinical Drug' = 'Blue colors',
    'Brand Name' = 'Red colors',
    'Branded Drug Comp' = 'Yellow colors',
    'Clinical Drug Comp' = 'Yellow colors',
    'Ingredient' = 'Red colors',
    'Multiple Ingredients' = 'Red colors',
    'Clinical Dose Group' = "Pink colors",
    'Branded Dose Group' = "Pink colors",
    'Dose Form Group' = "Pink colors",
    'Precise Ingredient' = 'Red colors',
    'Clinical Drug Form' = 'Purple, violet, and magenta colors',
    'Dose Form' = 'Purple, violet, and magenta colors',
    'Branded Drug Form' = 'Purple, violet, and magenta colors',
    'Branded Drug Box' = 'Brown colors',
    'Clinical Drug Box' = 'Brown colors',
    'Branded Pack Box' = 'Brown colors',
    'Clinical Pack Box' = 'Brown colors',
    'Quant Branded Box' = 'Brown colors',
    'Quant Clinical Box' = 'Brown colors',
    'Marketed Product' = 'Brown colors')


domain_color_groups <- 
c(
  'Condition'        = "Cyan colors",
  'Condition Status' = "Cyan colors",
  'Condition/Device' = "Cyan colors",
  'Condition/Meas'   = "Cyan colors",
  'Condition/Obs'    = "Cyan colors",
  'Condition/Procedure' = "Cyan colors",
  'Cost' = "White colors",
  'Currency' = "White colors",
  'Device' = "Purple, violet, and magenta colors", 
  'Device/Procedure' = "Purple, violet, and magenta colors",
  'Drug' = "Red colors",
  'Drug/Procedure' = "Red colors",
  'Episode' = "Blue colors",
  'Ethnicity' = "White colors",
  'Gender' = "White colors",
  'Geography' = "White colors",
  'Meas Value' = "Orange colors",
  'Meas Value Operator' = "Orange colors",
  'Measurement' = "Orange colors",
  'Metadata' = "Pink colors",
  'Obs/Procedure' = "Blue colors",
  'Observation' = "Blue colors",
  'Payer' = "White colors",
  'Place of Service' = "White colors",
  'Plan' = "White colors",
  'Plan Stop Reason' = "White colors",
  'Procedure' = "Yellow colors",
  'Provider' = "Green colors",
  'Race'  = "White colors",
  'Regimen' = "Red colors",
  'Relationship' = "Pink colors",
  'Revenue Code' = "Pink colors",
  'Route' = "Red colors",
  'Spec Anatomic Site' = "Blue colors",
  'Spec Disease Status' = "Blue colors",
  'Specimen' = "Brown colors",
  'Sponsor' = "Pink colors",
  'Type Concept' = "Pink colors",
  'Unit' = "Yellow colors",
  'Visit' = "Blue colors"
)

domain_colors <- 
c(
  `Condition` = c('aquamarine'),
  `Condition Status` = c('aquamarine'),
  `Condition/Device` = c('aquamarine'),
  `Condition/Meas` = c('aquamarine'),
  `Condition/Obs` = c('aquamarine'),
  `Condition/Procedure` = c('aquamarine'),
  `Cost` = c('honeydew'),
  `Currency` = c('honeydew'),
  `Device` = c('lightslateblue'),
  `Device/Procedure` = c('lightslateblue'),
  `Drug` = c('firebrick1'),
  `Drug/Procedure` = c('firebrick1'),
  `Episode` = c('dodgerblue'),
  `Ethnicity` = c('honeydew'),
  `Gender` = c('honeydew'),
  `Geography` = c('honeydew'),
  `Meas Value` = c('darkorange'),
  `Meas Value Operator` = c('darkorange'),
  `Measurement` = c('darkorange'),
  `Metadata` = c('tomato'),
  `Obs/Procedure` = c('dodgerblue'),
  `Observation` = c('dodgerblue'),
  `Payer` = c('honeydew'),
  `Place of Service` = c('honeydew'),
  `Plan` = c('honeydew'),
  `Plan Stop Reason` = c('honeydew'),
  `Procedure` = c('gold'),
  `Provider` = c('palegreen'),
  `Race` = c('honeydew'),
  `Regimen` = c('firebrick1'),
  `Relationship` = c('tomato'),
  `Revenue Code` = c('tomato'),
  `Route` = c('firebrick1'),
  `Spec Anatomic Site` = c('dodgerblue'),
  `Spec Disease Status` = c('dodgerblue'),
  `Specimen` = c('tan'),
  `Sponsor` = c('tomato'),
  `Type Concept` = c('tomato'),
  `Unit` = c('gold'),
  `Visit` = c('dodgerblue')
)


vocabulary_id_standard_colors <- 
list(
  `ATC` = c('goldenrod2'),
  `CIViC` = c('wheat2'),
  `CPT4` = c('blue2'),
  `Cancer Modifier` = c('royalblue2'),
  `ClinVar` = c('chartreuse2'),
  `Cohort` = c('chocolate2'),
  `Concept Class` = c('seashell2'),
  `Condition Status` = c('orchid2'),
  `Condition Type` = c('slateblue2'),
  `Cost` = c('firebrick2'),
  `Cost Type` = c('violetred2'),
  `Currency` = c('darkorange2'),
  `DRG` = c('mediumorchid2'),
  `Death Type` = c('sienna2'),
  `Device Type` = c('cornsilk2'),
  `Domain` = c('honeydew2'),
  `Drug Type` = c('lightgoldenrod2'),
  `EphMRA ATC` = c('azure2'),
  `Episode` = c('thistle2'),
  `Episode Type` = c('burlywood2'),
  `Ethnicity` = c('cadetblue2'),
  `GCN_SEQNO` = c('tan2'),
  `HCPCS` = c('orange2'),
  `HGNC` = c('lightcyan2'),
  `HemOnc` = c('cadetblue2'),
  `ICD10` = c('rosybrown2'),
  `ICD10CM` = c('indianred2'),
  `ICD10CN` = c('deepskyblue2'),
  `ICD10GM` = c('bisque2'),
  `ICD10PCS` = c('darkolivegreen2'),
  `ICD9CM` = c('palevioletred2'),
  `ICD9Proc` = c('pink2'),
  `ICD9ProcCN` = c('plum2'),
  `ICDO3` = c('peachpuff2'),
  `JAX` = c('mediumpurple2'),
  `LOINC` = c('seagreen2'),
  `MeSH` = c('steelblue2'),
  `Meas Type` = c('skyblue2'),
  `MedDRA` = c('red2'),
  `Metadata` = c('purple2'),
  `NAACCR` = c('paleturquoise2'),
  `NCIt` = c('yellow2'),
  `NDC` = c('magenta2'),
  `NDFRT` = c('dodgerblue2'),
  `Nebraska Lexicon` = c('gold2'),
  `None` = c('green2'),
  `OMOP Extension` = c('palegreen2'),
  `Observation Type` = c('tomato2'),
  `OncoKB` = c('lavenderblush2'),
  `PCORNet` = c('darkseagreen2'),
  `Race` = c('aquamarine2'),
  `Relationship` = c('lemonchiffon2'),
  `RxNorm` = c('deeppink2'),
  `RxNorm Extension` = c('mistyrose2'),
  `SNOMED` = c('lightskyblue2'),
  `Specimen Type` = c('olivedrab2'),
  `Type Concept` = c('salmon2'),
  `UCUM` = c('lightblue2'),
  `Vocabulary` = c('cyan2')
)

vocabulary_id_class_colors <- vocabulary_id_standard_colors

vocabulary_id_nonstandard_colors <- 
  list(
    `ATC` = c('goldenrod4'),
    `CIViC` = c('wheat4'),
    `CPT4` = c('blue4'),
    `Cancer Modifier` = c('royalblue4'),
    `ClinVar` = c('chartreuse4'),
    `Cohort` = c('chocolate4'),
    `Concept Class` = c('seashell4'),
    `Condition Status` = c('orchid4'),
    `Condition Type` = c('slateblue4'),
    `Cost` = c('firebrick4'),
    `Cost Type` = c('violetred4'),
    `Currency` = c('darkorange4'),
    `DRG` = c('mediumorchid4'),
    `Death Type` = c('sienna4'),
    `Device Type` = c('cornsilk4'),
    `Domain` = c('honeydew4'),
    `Drug Type` = c('lightgoldenrod4'),
    `EphMRA ATC` = c('azure4'),
    `Episode` = c('thistle4'),
    `Episode Type` = c('burlywood4'),
    `Ethnicity` = c('cadetblue4'),
    `GCN_SEQNO` = c('tan4'),
    `HCPCS` = c('orange4'),
    `HGNC` = c('lightcyan4'),
    `HemOnc` = c('maroon4'),
    `ICD10` = c('rosybrown4'),
    `ICD10CM` = c('indianred4'),
    `ICD10CN` = c('deepskyblue4'),
    `ICD10GM` = c('bisque4'),
    `ICD10PCS` = c('darkolivegreen4'),
    `ICD9CM` = c('palevioletred4'),
    `ICD9Proc` = c('pink4'),
    `ICD9ProcCN` = c('plum4'),
    `ICDO3` = c('peachpuff4'),
    `JAX` = c('mediumpurple4'),
    `LOINC` = c('seagreen4'),
    `MeSH` = c('steelblue4'),
    `Meas Type` = c('skyblue4'),
    `MedDRA` = c('red4'),
    `Metadata` = c('purple4'),
    `NAACCR` = c('paleturquoise4'),
    `NCIt` = c('yellow4'),
    `NDC` = c('magenta4'),
    `NDFRT` = c('dodgerblue4'),
    `Nebraska Lexicon` = c('gold4'),
    `None` = c('green4'),
    `OMOP Extension` = c('palegreen4'),
    `Observation Type` = c('tomato4'),
    `OncoKB` = c('lavenderblush4'),
    `PCORNet` = c('darkseagreen4'),
    `Race` = c('aquamarine4'),
    `Relationship` = c('lemonchiffon4'),
    `RxNorm` = c('deeppink4'),
    `RxNorm Extension` = c('mistyrose4'),
    `SNOMED` = c('lightskyblue4'),
    `Specimen Type` = c('olivedrab4'),
    `Type Concept` = c('salmon4'),
    `UCUM` = c('lightblue4'),
    `Vocabulary` = c('cyan4')
  )