From 4aae040ad22d2f10680c61688da187bed83e2ea0 Mon Sep 17 00:00:00 2001 From: Nardus Mollentze Date: Tue, 29 Jun 2021 10:07:04 +0100 Subject: [PATCH] Simplify installation - Moved to conda installation - Improved makefile/reproducibility --- .Rprofile | 1 - InternalData/NameChanges2019.csv | 862 +++++++++++ Makefile | 18 +- README.md | 112 +- Scripts/CalculateBaggedPredictions.R | 1 - .../MakeSupplement_FeatureSelection.R | 1 - .../MakeSupplement_HumanGeneSetSimilarity.R | 126 -- .../MakeSupplementaryFigure_EffectDirection.R | 4 +- .../MakeSupplementaryFigure_FeatureClusters.R | 4 +- Scripts/Plotting/PlottingConstants.R | 9 +- ...lement_TopFeatures_ComparedToHumanValues.R | 11 - Scripts/PredictNovel.R | 1 - Scripts/PredictNovel_PN.R | 1 - Scripts/TrainFamilyHeuristic.R | 5 +- Utils/PNsummary_utils.R | 3 +- Utils/calibration_utils.R | 9 +- base_environment.yml | 27 + dev_environment.yml | 30 + renv.lock | 1350 ----------------- ...osisPredictor.Rproj => zoonotic_rank.Rproj | 0 20 files changed, 1013 insertions(+), 1562 deletions(-) delete mode 100644 .Rprofile create mode 100644 InternalData/NameChanges2019.csv delete mode 100644 Scripts/Plotting/MakeSupplement_HumanGeneSetSimilarity.R delete mode 100644 Scripts/Plotting/Supplement_TopFeatures_ComparedToHumanValues.R mode change 100755 => 100644 Scripts/PredictNovel.R create mode 100644 base_environment.yml create mode 100644 dev_environment.yml delete mode 100644 renv.lock rename ZoonosisPredictor.Rproj => zoonotic_rank.Rproj (100%) diff --git a/.Rprofile b/.Rprofile deleted file mode 100644 index 81b960f..0000000 --- a/.Rprofile +++ /dev/null @@ -1 +0,0 @@ -source("renv/activate.R") diff --git a/InternalData/NameChanges2019.csv b/InternalData/NameChanges2019.csv new file mode 100644 index 0000000..0fff953 --- /dev/null +++ b/InternalData/NameChanges2019.csv @@ -0,0 +1,862 @@ +Name_2018b,Name_2019,Notes +Achimota pararubulavirus 1,Achimota pararubulavirus 1, +Achimota pararubulavirus 2,Achimota pararubulavirus 2, +Adelaide River ephemerovirus,Adelaide River ephemerovirus, +Adeno-associated dependoparvovirus A,Adeno-associated dependoparvovirus A, +Adeno-associated dependoparvovirus B,Adeno-associated dependoparvovirus B, +Grivet simian foamy virus,Grivet simian foamy virus, +African horse sickness virus,African horse sickness virus, +African swine fever virus,African swine fever virus, +Aichivirus A,Aichivirus A, +Akabane orthobunyavirus,Akabane orthobunyavirus, +Alagoas vesiculovirus,Alagoas vesiculovirus, +Alcelaphine gammaherpesvirus 1,Alcelaphine gammaherpesvirus 1, +Alcelaphine gammaherpesvirus 2,Alcelaphine gammaherpesvirus 2, +Allpahuayo mammarenavirus,Allpahuayo mammarenavirus, +Almpiwar sripuvirus,Almpiwar sripuvirus, +Alphacoronavirus 1,Alphacoronavirus 1, +Alphapapillomavirus 1,Alphapapillomavirus 1, +Alphapapillomavirus 10,Alphapapillomavirus 10, +Alphapapillomavirus 11,Alphapapillomavirus 11, +Alphapapillomavirus 12,Alphapapillomavirus 12, +Alphapapillomavirus 13,Alphapapillomavirus 13, +Alphapapillomavirus 14,Alphapapillomavirus 14, +Alphapapillomavirus 2,Alphapapillomavirus 2, +Alphapapillomavirus 3,Alphapapillomavirus 3, +Alphapapillomavirus 4,Alphapapillomavirus 4, +Alphapapillomavirus 5,Alphapapillomavirus 5, +Alphapapillomavirus 6,Alphapapillomavirus 6, +Alphapapillomavirus 7,Alphapapillomavirus 7, +Alphapapillomavirus 8,Alphapapillomavirus 8, +Alphapapillomavirus 9,Alphapapillomavirus 9, +Serra do Navio mammarenavirus,Serra do Navio mammarenavirus , +American bat vesiculovirus,American bat vesiculovirus, +Andes orthohantavirus,Andes orthohantavirus, +Anguillid perhabdovirus,Anguillid perhabdovirus, +Anopheles A orthobunyavirus,Anopheles A orthobunyavirus, +Apoi virus,Apoi virus, +Aquamavirus A,Aquamavirus A, +Aravan lyssavirus,Aravan lyssavirus, +Arboretum almendravirus,Arboretum almendravirus, +Aroa virus,Aroa virus, +Ateline alphaherpesvirus 1,Ateline alphaherpesvirus 1, +Aura virus,Aura virus, +Australian bat lyssavirus,Australian bat lyssavirus, +Avastrovirus 1,Avastrovirus 1, +Avastrovirus 2,Avastrovirus 2, +Avastrovirus 3,Avastrovirus 3, +Avian orthoavulavirus 1,Avian orthoavulavirus 1, +Avian metaavulavirus 10,Avian metaavulavirus 10, +Avian metaavulavirus 11,Avian metaavulavirus 11, +Avian orthoavulavirus 12,Avian orthoavulavirus 12, +Avian paraavulavirus 3,Avian paraavulavirus 3, +Avian paraavulavirus 4,Avian paraavulavirus 4, +Avian metaavulavirus 5,Avian metaavulavirus 5, +Avian metaavulavirus 6,Avian metaavulavirus 6, +Avian metaavulavirus 7,Avian metaavulavirus 7, +Avian metaavulavirus 8,Avian metaavulavirus 8, +Avian orthoavulavirus 9,Avian orthoavulavirus 9, +Avian coronavirus,Avian coronavirus, +Avian metapneumovirus,Avian metapneumovirus, +Avihepatovirus A,Avihepatovirus A, +Avisivirus B,Avisivirus B, +Avisivirus C,Avisivirus C, +Pestivirus I,Pestivirus I, +Baboon orthoreovirus,Baboon orthoreovirus, +Bagaza virus,Bagaza virus, +Banna virus,Banna virus, +Banzi virus,Banzi virus, +Barmah Forest virus,Barmah Forest virus, +Barur ledantevirus,Barur ledantevirus, +Bat coronavirus CDPHE15,Bat coronavirus CDPHE15, +Bat coronavirus HKU10,Bat coronavirus HKU10, +Bayou orthohantavirus,Bayou orthohantavirus, +Bear Canyon mammarenavirus,Bear Canyon mammarenavirus, +Bebaru virus,Bebaru virus, +Beluga whale coronavirus SW1,Beluga whale coronavirus SW1, +Berrimah ephemerovirus,Berrimah ephemerovirus, +Betacoronavirus 1,Betacoronavirus 1, +Betapapillomavirus 1,Betapapillomavirus 1, +Betapapillomavirus 2,Betapapillomavirus 2, +Betapapillomavirus 3,Betapapillomavirus 3, +Betapapillomavirus 4,Betapapillomavirus 4, +Betapapillomavirus 5,Betapapillomavirus 5, +Bimiti orthobunyavirus,Bimiti orthobunyavirus, +Bluetongue virus,Bluetongue virus, +Bokeloh bat lyssavirus,Bokeloh bat lyssavirus, +Pestivirus D,Pestivirus D, +Bos taurus polyomavirus 1,Bos taurus polyomavirus 1, +Bouboui virus,Bouboui virus, +Bovine alphaherpesvirus 1,Bovine alphaherpesvirus 1, +Bovine alphaherpesvirus 5,Bovine alphaherpesvirus 5, +Bovine atadenovirus D,Bovine atadenovirus D, +Bovine fever ephemerovirus,Bovine fever ephemerovirus, +Bovine foamy virus,Bovine foamy virus, +Bovine gammaherpesvirus 4,Bovine gammaherpesvirus 4, +Bovine immunodeficiency virus,Bovine immunodeficiency virus, +Bovine leukemia virus,Bovine leukemia virus, +Bovine mastadenovirus A,Bovine mastadenovirus A, +Bovine mastadenovirus B,Bovine mastadenovirus B, +Bovine mastadenovirus C,Bovine mastadenovirus C, +Bovine orthopneumovirus,Bovine orthopneumovirus, +Bovine papular stomatitis virus,Bovine papular stomatitis virus, +Bovine respirovirus 3,Bovine respirovirus 3, +Bovine torovirus,Bovine torovirus, +Pestivirus A,Pestivirus A, +Pestivirus B,Pestivirus B, +Pestivirus H,Pestivirus H, +Bubaline alphaherpesvirus 1,Bubaline alphaherpesvirus 1, +Bujaru phlebovirus,Bujaru phlebovirus, +Bundibugyo ebolavirus,Bundibugyo ebolavirus, +Bunyamwera orthobunyavirus,Bunyamwera orthobunyavirus, +Bwamba orthobunyavirus,Bwamba orthobunyavirus, +Cabassou virus,Cabassou virus, +Cacipacore virus,Cacipacore virus, +California encephalitis orthobunyavirus,California encephalitis orthobunyavirus, +California reptarenavirus,California reptarenavirus, +Callitrichine gammaherpesvirus 3,Callitrichine gammaherpesvirus 3, +Camelpox virus,Camelpox virus, +Candiru phlebovirus,Candiru phlebovirus, +Canid alphaherpesvirus 1,Canid alphaherpesvirus 1, +Canine mastadenovirus A,Canine mastadenovirus A, +Canine morbillivirus,Canine morbillivirus, +Cano Delgadito orthohantavirus,Cano Delgadito orthohantavirus, +Caprine arthritis encephalitis virus,Caprine arthritis encephalitis virus, +Caraparu orthobunyavirus,Caraparu orthobunyavirus, +Cardiovirus A,Cardiovirus A, +Cardiovirus B,Cardiovirus B, +Carnivore amdoparvovirus 1,Carnivore amdoparvovirus 1, +Carnivore bocaparvovirus 1,Carnivore bocaparvovirus 1, +Carnivore protoparvovirus 1,Carnivore protoparvovirus 1, +Carp sprivivirus,Carp sprivivirus, +Catu orthobunyavirus,Catu orthobunyavirus, +Caviid betaherpesvirus 2,Caviid betaherpesvirus 2, +Cedar henipavirus,Cedar henipavirus, +Cercopithecine alphaherpesvirus 2,Cercopithecine alphaherpesvirus 2, +Cercopithecine alphaherpesvirus 9,Cercopithecine alphaherpesvirus 9, +Cercopithecine betaherpesvirus 5,Cercopithecine betaherpesvirus 5, +Cervid alphaherpesvirus 1,Cervid alphaherpesvirus 1, +Cervid alphaherpesvirus 2,Cervid alphaherpesvirus 2, +Cetacean morbillivirus,Cetacean morbillivirus, +Chandipura vesiculovirus,Chandipura vesiculovirus, +Changuinola virus,Changuinola virus, +Chapare mammarenavirus,Chapare mammarenavirus, +Chikungunya virus,Chikungunya virus, +Chobar Gorge virus,Chobar Gorge virus, +Pestivirus C,Pestivirus C, +Coastal Plains tibrovirus,Coastal Plains tibrovirus, +Cocal vesiculovirus,Cocal vesiculovirus, +Colorado tick fever virus,Colorado tick fever coltivirus, +Common moorhen coronavirus HKU21,Common moorhen coronavirus HKU21, +Coronavirus HKU15,Coronavirus HKU15, +Corriparta virus,Corriparta virus, +Cowpox virus,Cowpox virus, +Crimean-Congo hemorrhagic fever orthonairovirus,Crimean-Congo hemorrhagic fever orthonairovirus, +Cupixi mammarenavirus,Cupixi mammarenavirus, +Curionopolis curiovirus,Curionopolis curiovirus, +Deltapapillomavirus 1,Deltapapillomavirus 1, +Deltapapillomavirus 2,Deltapapillomavirus 2, +Deltapapillomavirus 3,Deltapapillomavirus 3, +Deltapapillomavirus 4,Deltapapillomavirus 4, +Dengue virus,Dengue virus, +Dera Ghazi Khan orthonairovirus,Dera Ghazi Khan orthonairovirus, +Dhori thogotovirus,Dhori thogotovirus, +Dobrava-Belgrade orthohantavirus,Dobrava-Belgrade orthohantavirus, +Drosophila melanogaster sigmavirus,Drosophila melanogaster sigmavirus, +Drosophila obscura sigmavirus,Drosophila obscura sigmavirus, +Aalivirus A,Aalivirus A, +Dugbe orthonairovirus,Dugbe orthonairovirus, +Duvenhage lyssavirus,Duvenhage lyssavirus, +Eastern equine encephalitis virus,Eastern equine encephalitis virus, +Ectromelia virus,Ectromelia virus, +Eggplant mottled dwarf nucleorhabdovirus,Eggplant mottled dwarf alphanucleorhabdovirus, +Eilat virus,Eilat virus, +Entebbe bat virus,Entebbe bat virus, +Enterovirus A,Enterovirus A, +Enterovirus B,Enterovirus B, +Enterovirus C,Enterovirus C, +Enterovirus D,Enterovirus D, +Enterovirus G,Enterovirus G, +Enterovirus H,Enterovirus H, +Enterovirus I,Enterovirus I, +Epizootic hemorrhagic disease virus,Epizootic hemorrhagic disease virus, +Epsilonpapillomavirus 1,Epsilonpapillomavirus 1, +Equid alphaherpesvirus 1,Equid alphaherpesvirus 1, +Equid alphaherpesvirus 3,Equid alphaherpesvirus 3, +Equid alphaherpesvirus 4,Equid alphaherpesvirus 4, +Equid alphaherpesvirus 8,Equid alphaherpesvirus 8, +Equid alphaherpesvirus 9,Equid alphaherpesvirus 9, +Equid gammaherpesvirus 2,Equid gammaherpesvirus 2, +Equid gammaherpesvirus 5,Equid gammaherpesvirus 5, +Alphaarterivirus equid,Alphaarterivirus equid, +Equine encephalosis virus,Equine encephalosis virus, +Equine foamy virus,Equine foamy virus, +Equine infectious anemia virus,Equine infectious anemia virus, +Equine mastadenovirus A,Equine mastadenovirus A, +Equine mastadenovirus B,Equine mastadenovirus B, +Equine rhinitis A virus,Equine rhinitis A virus, +Equine torovirus,Equine torovirus, +Erbovirus A,Erbovirus A, +Eubenangee virus,Eubenangee virus, +European bat 1 lyssavirus,European bat 1 lyssavirus, +European bat 2 lyssavirus,European bat 2 lyssavirus, +European brown hare syndrome virus,European brown hare syndrome virus, +Everglades virus,Everglades virus, +Eyach virus,Eyach coltivirus, +Felid alphaherpesvirus 1,Felid alphaherpesvirus 1, +Feline calicivirus,Feline calicivirus, +Feline foamy virus,Feline foamy virus, +Feline immunodeficiency virus,Feline immunodeficiency virus, +Feline leukemia virus,Feline leukemia virus, +Feline morbillivirus,Feline morbillivirus, +Ferak feravirus,Ferak feravirus, +Fikirini ledantevirus,Fikirini ledantevirus, +Flexal mammarenavirus,Flexal mammarenavirus, +Foot-and-mouth disease virus,Foot-and-mouth disease virus, +Fort Morgan virus,Fort Morgan virus, +Gairo mammarenavirus,Gairo mammarenavirus, +Gammapapillomavirus 1,Gammapapillomavirus 1, +Gammapapillomavirus 2,Gammapapillomavirus 2, +Gammapapillomavirus 3,Gammapapillomavirus 3, +Gammapapillomavirus 4,Gammapapillomavirus 4, +Gammapapillomavirus 5,Gammapapillomavirus 5, +Getah virus,Getah virus, +Ghanaian bat henipavirus,Ghanaian bat henipavirus, +Gibbon ape leukemia virus,Gibbon ape leukemia virus, +Goatpox virus,Goatpox virus, +Golden reptarenavirus,Golden reptarenavirus, +Gouleako goukovirus,Gouleako goukovirus, +Great Island virus,Great Island virus, +Ground squirrel hepatitis virus,Ground squirrel hepatitis virus, +Guama orthobunyavirus,Guama orthobunyavirus, +Guanarito mammarenavirus,Guanarito mammarenavirus, +Guaroa orthobunyavirus,Guaroa orthobunyavirus, +Hantaan orthohantavirus,Hantaan orthohantavirus, +Harkavirus A,Harkavirus A, +Hedgehog coronavirus 1,Hedgehog coronavirus 1, +Hendra henipavirus,Hendra henipavirus, +Hepacivirus C,Hepacivirus C, +Hepatitis B virus,Hepatitis B virus, +Hepatovirus A,Hepatovirus A, +Hepatovirus B,Hepatovirus B, +Herbert herbevirus,Herbert herbevirus, +Highlands J virus,Highlands J virus, +Hirame novirhabdovirus,Hirame novirhabdovirus, +Human alphaherpesvirus 1,Human alphaherpesvirus 1, +Human alphaherpesvirus 2,Human alphaherpesvirus 2, +Human alphaherpesvirus 3,Human alphaherpesvirus 3, +Human betaherpesvirus 5,Human betaherpesvirus 5, +Human betaherpesvirus 7,Human betaherpesvirus 7, +Human coronavirus 229E,Human coronavirus 229E, +Human coronavirus HKU1,Human coronavirus HKU1, +Human coronavirus NL63,Human coronavirus NL63, +Human gammaherpesvirus 4,Human gammaherpesvirus 4, +Human gammaherpesvirus 8,Human gammaherpesvirus 8, +Human immunodeficiency virus 1,Human immunodeficiency virus 1, +Human immunodeficiency virus 2,Human immunodeficiency virus 2, +Human mastadenovirus A,Human mastadenovirus A, +Human mastadenovirus B,Human mastadenovirus B, +Human mastadenovirus C,Human mastadenovirus C, +Human mastadenovirus D,Human mastadenovirus D, +Human mastadenovirus E,Human mastadenovirus E, +Human mastadenovirus F,Human mastadenovirus F, +Human metapneumovirus,Human metapneumovirus, +Human orthopneumovirus,Human orthopneumovirus, +Human picobirnavirus,Human picobirnavirus, +Human polyomavirus 1,Human polyomavirus 1, +Human polyomavirus 2,Human polyomavirus 2, +Human respirovirus 1,Human respirovirus 1, +Human respirovirus 3,Human respirovirus 3, +Human orthorubulavirus 2,Human orthorubulavirus 2, +Human orthorubulavirus 4,Human orthorubulavirus 4, +Ikoma lyssavirus,Ikoma lyssavirus, +Ilheus virus,Ilheus virus, +Indiana vesiculovirus,Indiana vesiculovirus, +Influenza A virus,Influenza A virus, +Influenza B virus,Influenza B virus, +Influenza C virus,Influenza C virus, +Iotapapillomavirus 1,Iotapapillomavirus 1, +Ippy mammarenavirus,Ippy mammarenavirus, +Irkut lyssavirus,Irkut lyssavirus, +Isfahan vesiculovirus,Isfahan vesiculovirus, +Jaagsiekte sheep retrovirus,Jaagsiekte sheep retrovirus, +Japanese encephalitis virus,Japanese encephalitis virus, +Jonchet jonvirus,Jonchet jonvirus, +Jugra virus,Jugra virus, +Argentinian mammarenavirus,Argentinian mammarenavirus, +Jurona vesiculovirus,Jurona vesiculovirus, +Jutiapa virus,Jutiapa virus, +Kaeng Khoi orthobunyavirus,Kaeng Khoi orthobunyavirus, +Kairi orthobunyavirus,Kairi orthobunyavirus, +Kappapapillomavirus 1,Kappapapillomavirus 1, +Kappapapillomavirus 2,Kappapapillomavirus 2, +Kasokero orthonairovirus,Kasokero orthonairovirus, +Kedougou virus,Kedougou virus, +Kern Canyon ledantevirus,Kern Canyon ledantevirus, +Keuraliba ledantevirus,Keuraliba ledantevirus, +Khabarovsk orthohantavirus,Khabarovsk orthohantavirus, +Khujand lyssavirus,Khujand lyssavirus, +Kimberley ephemerovirus,Kimberley ephemerovirus, +Kokobera virus,Kokobera virus, +Kolente ledantevirus,Kolente ledantevirus, +Koongol orthobunyavirus,Koongol orthobunyavirus, +Kotonkan ephemerovirus,Kotonkan ephemerovirus, +Koutango virus,Koutango virus, +Kyasanur Forest disease virus,Kyasanur Forest disease virus, +Gammaarterivirus lacdeh,Gammaarterivirus lacdeh, +Lagos bat lyssavirus,Lagos bat lyssavirus, +Lambdapapillomavirus 1,Lambdapapillomavirus 1, +Lambdapapillomavirus 2,Lambdapapillomavirus 2, +Langat virus,Langat virus, +Lassa mammarenavirus,Lassa mammarenavirus, +Latino mammarenavirus,Latino mammarenavirus, +Lebombo virus,Lebombo virus, +Lettuce necrotic yellows cytorhabdovirus,Lettuce necrotic yellows cytorhabdovirus, +Lettuce yellow mottle cytorhabdovirus,Lettuce yellow mottle cytorhabdovirus, +Limnipivirus C,Limnipivirus C, +Lloviu cuevavirus,Lloviu cuevavirus, +Loei River mammarenavirus,Loei River mammarenavirus, +Louping ill virus,Louping ill virus, +Lujo mammarenavirus,Lujo mammarenavirus, +Lumpy skin disease virus,Lumpy skin disease virus, +Luna mammarenavirus,Luna mammarenavirus, +Lunk mammarenavirus,Lunk mammarenavirus, +Lymphocytic choriomeningitis mammarenavirus,Lymphocytic choriomeningitis mammarenavirus, +Macaca mulatta polyomavirus 1,Macaca mulatta polyomavirus 1, +Macacine alphaherpesvirus 1,Macacine alphaherpesvirus 1, +Macacine betaherpesvirus 3,Macacine betaherpesvirus 3, +Macacine gammaherpesvirus 4,Macacine gammaherpesvirus 4, +Macacine gammaherpesvirus 5,Macacine gammaherpesvirus 5, +Rhesus macaque simian foamy virus,Rhesus macaque simian foamy virus, +Machupo mammarenavirus,Machupo mammarenavirus, +Macropodid alphaherpesvirus 1,Macropodid alphaherpesvirus 1, +Madariaga virus,Madariaga virus, +Madrid orthobunyavirus,Madrid orthobunyavirus, +Main Drain orthobunyavirus,Main Drain orthobunyavirus, +Maize fine streak nucleorhabdovirus,Maize fine streak gammanucleorhabdovirus, +Maize Iranian mosaic nucleorhabdovirus,Maize Iranian mosaic alphanucleorhabdovirus, +Maize mosaic nucleorhabdovirus,Maize mosaic alphanucleorhabdovirus, +Malpais Spring vesiculovirus,Malpais Spring vesiculovirus, +Mamastrovirus 1,Mamastrovirus 1, +Mamastrovirus 10,Mamastrovirus 10, +Mamastrovirus 13,Mamastrovirus 13, +Mamastrovirus 2,Mamastrovirus 2, +Mamastrovirus 3,Mamastrovirus 3, +Mamastrovirus 6,Mamastrovirus 6, +Mamastrovirus 9,Mamastrovirus 9, +Mammalian 1 orthobornavirus,Mammalian 1 orthobornavirus, +Mammalian orthorubulavirus 5,Mammalian orthorubulavirus 5, +Manzanilla orthobunyavirus,Manzanilla orthobunyavirus, +Mapuera orthorubulavirus,Mapuera orthorubulavirus, +Maraba vesiculovirus,Maraba vesiculovirus, +Marburg marburgvirus,Marburg marburgvirus, +Marituba orthobunyavirus,Marituba orthobunyavirus, +Mason-Pfizer monkey virus,Mason-Pfizer monkey virus, +Mayaro virus,Mayaro virus, +Measles morbillivirus,Measles morbillivirus, +Menangle pararubulavirus,Menangle pararubulavirus, +Merino Walk mammarenavirus,Merino Walk mammarenavirus, +Mesocricetus auratus polyomavirus 1,Mesocricetus auratus polyomavirus 1, +Middelburg virus,Middelburg virus, +Middle East respiratory syndrome-related coronavirus,Middle East respiratory syndrome-related coronavirus, +Miniopterus bat coronavirus HKU8,Miniopterus bat coronavirus HKU8, +Mischivirus A,Mischivirus A, +Mischivirus C,Mischivirus C, +Mobala mammarenavirus,Mobala mammarenavirus, +Modoc virus,Modoc virus, +Mojiang henipavirus,Mojiang henipavirus, +Mokola lyssavirus,Mokola lyssavirus, +Molluscum contagiosum virus,Molluscum contagiosum virus, +Moloney murine sarcoma virus,Moloney murine sarcoma virus, +Monkeypox virus,Monkeypox virus, +Montana myotis leukoencephalitis virus,Montana myotis leukoencephalitis virus, +Mopeia mammarenavirus,Mopeia mammarenavirus, +Mosso das Pedras virus,Mosso das Pedras virus, +Mount Elgon bat ledantevirus,Mount Elgon bat ledantevirus, +Mouse mammary tumor virus,Mouse mammary tumor virus, +Moussa virus,Moussa mousrhavirus, +Mucambo virus,Mucambo virus, +Mumps orthorubulavirus,Mumps orthorubulavirus, +Munia coronavirus HKU13,Munia coronavirus HKU13, +Mupapillomavirus 1,Mupapillomavirus 1, +Mupapillomavirus 2,Mupapillomavirus 2, +Murid betaherpesvirus 1,Murid betaherpesvirus 1, +Murid betaherpesvirus 2,Murid betaherpesvirus 2, +Murid gammaherpesvirus 4,Murid gammaherpesvirus 4, +Murine coronavirus,Murine coronavirus, +Murine leukemia virus,Murine leukemia virus, +Murine mastadenovirus A,Murine mastadenovirus A, +Murine mastadenovirus B,Murine mastadenovirus B, +Murine orthopneumovirus,Murine orthopneumovirus, +Murine respirovirus,Murine respirovirus, +Murray Valley encephalitis virus,Murray Valley encephalitis virus, +Mus musculus polyomavirus 1,Mus musculus polyomavirus 1, +Mus musculus polyomavirus 2,Mus musculus polyomavirus 2, +Myxoma virus,Myxoma virus, +Ndumu virus,Ndumu virus, +Nelson Bay orthoreovirus,Nelson Bay orthoreovirus, +New Jersey vesiculovirus,New Jersey vesiculovirus, +Newbury 1 virus,Newbury 1 virus, +Ngaingan hapavirus,Ngaingan hapavirus, +Niakha sripuvirus,Niakha sripuvirus, +Night heron coronavirus HKU19,Night heron coronavirus HKU19, +Nipah henipavirus,Nipah henipavirus, +Northern cereal mosaic cytorhabdovirus,Northern cereal mosaic cytorhabdovirus, +Norwalk virus,Norwalk virus, +Ntaya virus,Ntaya virus, +Nupapillomavirus 1,Nupapillomavirus 1, +Nyando orthobunyavirus,Nyando orthobunyavirus, +Onyong-nyong virus,Onyong-nyong virus, +Obodhiang ephemerovirus,Obodhiang ephemerovirus, +Oita ledantevirus,Oita ledantevirus, +Oliveros mammarenavirus,Oliveros mammarenavirus, +Omikronpapillomavirus 1,Omikronpapillomavirus 1, +Omsk hemorrhagic fever virus,Omsk hemorrhagic fever virus, +Orf virus,Orf virus, +Oriboca orthobunyavirus,Oriboca orthobunyavirus, +Oropouche orthobunyavirus,Oropouche orthobunyavirus, +Orthohepevirus A,Orthohepevirus A, +Orthohepevirus B,Orthohepevirus B, +Orthohepevirus C,Orthohepevirus C, +Orthohepevirus D,Orthohepevirus D, +Orungo virus,Orungo virus, +Oscivirus A,Oscivirus A, +Ovine atadenovirus D,Ovine atadenovirus D, +Ovine gammaherpesvirus 2,Ovine gammaherpesvirus 2, +Ovine mastadenovirus A,Ovine mastadenovirus A, +Palyam virus,Palyam virus, +Panine betaherpesvirus 2,Panine betaherpesvirus 2, +Papiine alphaherpesvirus 2,Papiine alphaherpesvirus 2, +Paraguayan mammarenavirus,Paraguayan mammarenavirus, +Parapoxvirus of red deer in New Zealand,Red deerpox virus, +Parechovirus A,Parechovirus A, +Parechovirus B,Parechovirus B, +Patois orthobunyavirus,Patois orthobunyavirus, +Pegivirus A,Pegivirus A, +Pegivirus C,Pegivirus C, +Pegivirus E,Pegivirus E, +Pegivirus H,Pegivirus H, +Perch perhabdovirus,Perch perhabdovirus, +Perinet vesiculovirus,Perinet vesiculovirus, +Peruvian horse sickness virus,Peruvian horse sickness virus, +Phnom Penh bat virus,Phnom Penh bat virus, +Phocid alphaherpesvirus 1,Phocid alphaherpesvirus 1, +Phocine morbillivirus,Phocine morbillivirus, +Cali mammarenavirus,Cali mammarenavirus, +Pipapillomavirus 1,Pipapillomavirus 1, +Pipistrellus bat coronavirus HKU5,Pipistrellus bat coronavirus HKU5, +Pirital mammarenavirus,Pirital mammarenavirus, +Piry vesiculovirus,Piry vesiculovirus, +Piscihepevirus A,Piscihepevirus A, +Piscine novirhabdovirus,Piscine novirhabdovirus, +Pixuna virus,Pixuna virus, +Porcine circovirus 1,Porcine circovirus 1, +Porcine circovirus 2,Porcine circovirus 2, +Porcine epidemic diarrhea virus,Porcine epidemic diarrhea virus, +Porcine mastadenovirus A,Porcine mastadenovirus A, +Porcine mastadenovirus C,Porcine mastadenovirus C, +Betaarterivirus suid 1,Betaarterivirus suid 1, +Porcine respirovirus 1,Porcine respirovirus 1, +Porcine orthorubulavirus,Porcine orthorubulavirus, +Porcine torovirus,Porcine torovirus, +Porcine type-C oncovirus,Porcine type-C oncovirus, +Potato yellow dwarf nucleorhabdovirus,Potato yellow dwarf alphanucleorhabdovirus, +Powassan virus,Powassan virus, +Primate erythroparvovirus 1,Primate erythroparvovirus 1, +Primate T-lymphotropic virus 1,Primate T-lymphotropic virus 1, +Primate T-lymphotropic virus 2,Primate T-lymphotropic virus 2, +Primate T-lymphotropic virus 3,Primate T-lymphotropic virus 3, +Pestivirus E,Pestivirus E, +Pseudocowpox virus,Pseudocowpox virus, +Puerto Almendras almendravirus,Puerto Almendras almendravirus, +Puma lentivirus,Puma lentivirus, +Punta Toro phlebovirus,Punta Toro phlebovirus, +Puumala orthohantavirus,Puumala orthohantavirus, +Quaranfil quaranjavirus,Quaranfil quaranjavirus, +Rabbit fibroma virus,Rabbit fibroma virus, +Rabbit hemorrhagic disease virus,Rabbit hemorrhagic disease virus, +Rabies lyssavirus,Rabies lyssavirus, +Raccoonpox virus,Raccoonpox virus, +Reptile sunshinevirus 1,Reptile sunshinevirus 1, +Reptilian ferlavirus,Reptilian ferlavirus, +Reston ebolavirus,Reston ebolavirus, +Rhinolophus bat coronavirus HKU2,Rhinolophus bat coronavirus HKU2, +Rhinovirus A,Rhinovirus A, +Rhinovirus B,Rhinovirus B, +Rhinovirus C,Rhinovirus C, +Rice yellow stunt nucleorhabdovirus,Rice yellow stunt alphanucleorhabdovirus, +Rift Valley fever phlebovirus,Rift Valley fever phlebovirus, +Rinderpest morbillivirus,Rinderpest morbillivirus, +Rio Bravo virus,Rio Bravo virus, +Rio Negro virus,Rio Negro virus, +Rodent erythroparvovirus 1,Rodent erythroparvovirus 1, +Rodent protoparvovirus 1,Rodent protoparvovirus 1, +Rodent protoparvovirus 2,Rodent protoparvovirus 2, +Ross River virus,Ross River virus, +Rotavirus A,Rotavirus A, +Rotavirus B,Rotavirus B, +Rotavirus C,Rotavirus C, +Rotterdam reptarenavirus,Rotterdam reptarenavirus, +Rousettus bat coronavirus HKU9,Rousettus bat coronavirus HKU9, +Royal Farm virus,Royal Farm virus, +Rubella virus,Rubella virus, +Brazilian mammarenavirus,Brazilian mammarenavirus, +Saboya virus,Saboya virus, +Saimiriine alphaherpesvirus 1,Saimiriine alphaherpesvirus 1, +Saimiriine gammaherpesvirus 2,Saimiriine gammaherpesvirus 2, +Sakobuvirus A,Sakobuvirus A, +Salehabad phlebovirus,Salehabad phlebovirus, +Salivirus A,Salivirus A, +Salmon aquaparamyxovirus,Salmo aquaparamyxovirus, +Salmon pancreas disease virus,Salmon pancreas disease virus, +Salmonid novirhabdovirus,Salmonid novirhabdovirus, +Sandfly fever Naples phlebovirus,Naples phlebovirus, +Sapelovirus A,Sapelovirus A, +Sapporo virus,Sapporo virus, +Scotophilus bat coronavirus 512,Scotophilus bat coronavirus 512, +Semliki Forest virus,Semliki Forest virus, +Seoul orthohantavirus,Seoul orthohantavirus, +Sepik virus,Sepik virus, +Severe acute respiratory syndrome-related coronavirus,Severe acute respiratory syndrome-related coronavirus, +Huaiyangshan banyangvirus,Dabie bandavirus, +Schmallenberg orthobunyavirus,Schmallenberg orthobunyavirus, +Sheeppox virus,Sheeppox virus, +Shimoni bat lyssavirus,Shimoni bat lyssavirus, +Shuni orthobunyavirus,Shuni orthobunyavirus, +Sicinivirus A,Sicinivirus A, +Simbu orthobunyavirus,Simbu orthobunyavirus, +Western chimpanzee simian foamy virus,Western chimpanzee simian foamy virus, +Deltaarterivirus hemfev,Deltaarterivirus hemfev, +Simian immunodeficiency virus,Simian immunodeficiency virus, +Simian orthorubulavirus,Simian orthorubulavirus, +Sin Nombre orthohantavirus,Sin Nombre orthohantavirus, +Sindbis virus,Sindbis virus, +Small ruminant morbillivirus,Small ruminant morbillivirus, +Snakehead novirhabdovirus,Snakehead novirhabdovirus, +Sonchus yellow net nucleorhabdovirus,Sonchus yellow net betanucleorhabdovirus, +Sosuga pararubulavirus,Sosuga pararubulavirus, +Southern elephant seal virus,Southern elephant seal virus, +Squirrel monkey retrovirus,Squirrel monkey retrovirus, +Squirrelpox virus,Squirrelpox virus, +Saint Louis encephalitis virus,Saint Louis encephalitis virus, +Sudan ebolavirus,Sudan ebolavirus, +Suid alphaherpesvirus 1,Suid alphaherpesvirus 1, +Swinepox virus,Swinepox virus, +Tacaiuma orthobunyavirus,Tacaiuma orthobunyavirus, +Tacaribe mammarenavirus,Tacaribe mammarenavirus, +Tai Forest ebolavirus,Tai Forest ebolavirus, +Tamiami mammarenavirus,Tamiami mammarenavirus, +Tanapox virus,Tanapox virus, +Taro vein chlorosis nucleorhabdovirus,Taro vein chlorosis alphanucleorhabdovirus, +Taterapox virus,Taterapox virus, +Tembusu virus,Tembusu virus, +Pike fry sprivivirus,Pike fry sprivivirus, +Teschovirus A,Teschovirus A, +Thailand orthohantavirus,Thailand orthohantavirus, +Thiafora orthonairovirus,Thiafora orthonairovirus, +Thogoto thogotovirus,Thogoto thogotovirus, +Thottopalayam thottimvirus,Thottopalayam thottimvirus, +Tibrogargan tibrovirus,Tibrogargan tibrovirus, +Tick-borne encephalitis virus,Tick-borne encephalitis virus, +Tioman pararubulavirus,Tioman pararubulavirus, +Tonate virus,Tonate virus, +Tree shrew mastadenovirus A,Tree shrew mastadenovirus A, +Tremovirus A,Tremovirus A, +Tuhoko pararubulavirus 1,Tuhoko pararubulavirus 1, +Tuhoko pararubulavirus 2,Tuhoko pararubulavirus 2, +Tuhoko pararubulavirus 3,Tuhoko pararubulavirus 3, +Tula orthohantavirus,Tula orthohantavirus, +Tupaia tupavirus,Tupaia tupavirus, +Tupaiid betaherpesvirus 1,Tupaiid betaherpesvirus 1, +Turlock orthobunyavirus,Turlock orthobunyavirus, +Tylonycteris bat coronavirus HKU4,Tylonycteris bat coronavirus HKU4, +Tyuleniy virus,Tyuleniy virus, +Uganda S virus,Uganda S virus, +Una virus,Una virus, +Ungulate bocaparvovirus 1,Ungulate bocaparvovirus 1, +Ungulate protoparvovirus 1,Ungulate protoparvovirus 1, +Uukuniemi phlebovirus,Uukuniemi uukuvirus, +Variola virus,Variola virus, +Venezuelan equine encephalitis virus,Venezuelan equine encephalitis virus, +Vesicular exanthema of swine virus,Vesicular exanthema of swine virus, +Visna-maedi virus,Visna-maedi virus, +Volepox virus,Volepox virus, +Wad Medani virus,Wad Medani virus, +Wallal virus,Wallal virus, +Warrego virus,Warrego virus, +Wenzhou mammarenavirus,Wenzhou mammarenavirus, +Wesselsbron virus,Wesselsbron virus, +West Caucasian bat lyssavirus,West Caucasian bat lyssavirus, +West Nile virus,West Nile virus, +Western equine encephalitis virus,Western equine encephalitis virus, +Whataroa virus,Whataroa virus, +White bream virus,White bream virus, +White-eye coronavirus HKU16,White-eye coronavirus HKU16, +Whitewater Arroyo mammarenavirus,Whitewater Arroyo mammarenavirus, +Wigeon coronavirus HKU20,Wigeon coronavirus HKU20, +Wongabel hapavirus,Wongabel hapavirus, +Woodchuck hepatitis virus,Woodchuck hepatitis virus, +Woolly monkey sarcoma virus,Woolly monkey sarcoma virus, +Wyeomyia orthobunyavirus,Wyeomyia orthobunyavirus, +Xipapillomavirus 1,Xipapillomavirus 1, +Yaba monkey tumor virus,Yaba monkey tumor virus, +Yellow fever virus,Yellow fever virus, +Yokose virus,Yokose virus, +Yug Bogdanovac vesiculovirus,Yug Bogdanovac vesiculovirus, +Zaire ebolavirus,Zaire ebolavirus, +Zegla orthobunyavirus,Zegla orthobunyavirus, +Zetapapillomavirus 1,Zetapapillomavirus 1, +Zika virus,Zika virus, +Choclo orthohantavirus,Choclo orthohantavirus, +Ekpoma 1 tibrovirus,Ekpoma 1 tibrovirus, +Ekpoma 2 tibrovirus,Ekpoma 2 tibrovirus, +Mammalian 2 orthobornavirus,Mammalian 2 orthobornavirus, +Rotavirus H,Rotavirus H, +Aedes pseudoscutellaris reovirus,Aedes pseudoscutellaris reovirus, +Lambdaarterivirus afriporav,Lambdaarterivirus afriporav, +Aichivirus B,Aichivirus B, +Aichivirus C,Aichivirus C, +Aichivirus D,Aichivirus D, +Aichivirus E,Aichivirus E, +Aichivirus F,Aichivirus F, +Alajuela orthobunyavirus,Alajuela orthobunyavirus, +Alfalfa dwarf cytorhabdovirus,Alfalfa dwarf cytorhabdovirus, +Ampivirus A,Ampivirus A, +Aquareovirus A,Aquareovirus A, +Aquareovirus B,Aquareovirus B, +Aquareovirus C,Aquareovirus C, +Aquareovirus E,Aquareovirus E, +Aquareovirus G,Aquareovirus G, +Avian orthoavulavirus 13,Avian orthoavulavirus 13, +Avian metaavulavirus 2,Avian metaavulavirus 2, +Avian leukosis virus,Avian leukosis virus, +Avian orthoreovirus,Avian orthoreovirus, +Anativirus A,Anativirus A, +Avisivirus A,Avisivirus A, +Badu phasivirus,Badu phasivirus, +Ball python nidovirus 1,Ball python nidovirus 1, +Barley yellow striate mosaic cytorhabdovirus,Barley yellow striate mosaic cytorhabdovirus, +Bat mumps orthorubulavirus,Mumps orthorubulavirus,Species abolished – reason given is that it’s not distinct enough from Mumps orthorubulavirus +Batama orthobunyavirus,Batama orthobunyavirus, +Bertioga orthobunyavirus,Bertioga orthobunyavirus, +Bovine nidovirus 1,Bovine nidovirus 1, +Bovine rhinitis A virus,Bovine rhinitis A virus, +Bovine rhinitis B virus,Bovine rhinitis B virus, +Bowe orthohantavirus,Bowe orthohantavirus, +Bruges orthohantavirus,Bruges orthohantavirus, +Bulbul coronavirus HKU11,Bulbul coronavirus HKU11, +Tamdy orthonairovirus,Tamdy orthonairovirus, +Cadicivirus A,Cadicivirus A, +Cao Bang orthohantavirus,Cao Bang orthohantavirus, +Capim orthobunyavirus,Capim orthobunyavirus, +Carajas vesiculovirus,Carajas vesiculovirus, +Cardiovirus C,Cardiovirus C, +Chaco sripuvirus,Chaco sripuvirus, +Chenuda virus,Chenuda virus, +Chilibre phlebovirus,Chilibre pacuvirus, +Chinook salmon nidovirus 1,Chinook salmon nidovirus 1, +Coffee ringspot dichorhavirus,Coffee ringspot dichorhavirus, +Colocasia bobone disease-associated cytorhabdovirus,Colocasia bobone disease-associated cytorhabdovirus, +Cosavirus A,Cosavirus A, +Cosavirus B,Cosavirus B, +Cosavirus D,Cosavirus D, +Cosavirus E,Cosavirus E, +Cosavirus F,Cosavirus F, +Cumuto goukovirus,Cumuto goukovirus, +Cypovirus 1,Cypovirus 1, +Cypovirus 14,Cypovirus 14, +Cypovirus 15,Cypovirus 15, +Cypovirus 2,Cypovirus 2, +Cypovirus 5,Cypovirus 5, +Dabieshan orthohantavirus,Dabieshan orthohantavirus, +Datura yellow vein nucleorhabdovirus,Datura yellow vein betanucleorhabdovirus, +Iotaarterivirus debrazmo,Iotaarterivirus debrazmo, +Drosophila affinis sigmavirus,Drosophila affinis sigmavirus, +Drosophila ananassae sigmavirus,Drosophila ananassae sigmavirus, +Drosophila immigrans sigmavirus,Drosophila immigrans sigmavirus, +Drosophila X virus,Drosophila X virus, +Durham tupavirus,Durham tupavirus, +Edge Hill virus,Edge Hill virus, +Elapid 1 orthobornavirus,Elapid 1 orthobornavirus, +Enterovirus E,Enterovirus E, +Enterovirus F,Enterovirus F, +Enterovirus J,Enterovirus J, +Eriocheir sinensis reovirus,Eriocheir sinensis reovirus, +Estero Real orthonairovirus,Estero Real orthonairovirus, +Fathead minnow nidovirus 1,Fathead minnow nidovirus 1, +Fiji disease virus,Fiji disease virus, +Flanders hapavirus,Flanders hapavirus, +Epsilonarterivirus safriver,Epsilonarterivirus safriver, +Frijoles phlebovirus,Frijoles phlebovirus, +Fugong orthohantavirus,Fugong orthohantavirus, +Fukuoka ledantevirus,Fukuoka ledantevirus, +Fusong orthohantavirus,Fusong orthohantavirus, +Gadgets Gully virus,Gadgets Gully virus, +Gallivirus A,Gallivirus A, +Gamboa orthobunyavirus,Gamboa orthobunyavirus, +Gray Lodge hapavirus,Gray Lodge hapavirus, +Guajara orthobunyavirus,Guajara orthobunyavirus, +Hart Park hapavirus,Hart Park hapavirus, +Hazara orthonairovirus,Hazara orthonairovirus, +Hepacivirus A,Hepacivirus A, +Hepacivirus B,Hepacivirus B, +Hepacivirus D,Hepacivirus D, +Hepacivirus E,Hepacivirus E, +Hepacivirus F,Hepacivirus F, +Hepacivirus G,Hepacivirus G, +Hepacivirus H,Hepacivirus H, +Hepacivirus I,Hepacivirus I, +Hepacivirus J,Hepacivirus J, +Hepacivirus K,Hepacivirus K, +Hepacivirus L,Hepacivirus L, +Hepacivirus M,Hepacivirus M, +Hepacivirus N,Hepacivirus N, +Hepatovirus C,Hepatovirus C, +Hepatovirus D,Hepatovirus D, +Hepatovirus E,Hepatovirus E, +Hepatovirus F,Hepatovirus F, +Hepatovirus G,Hepatovirus G, +Hepatovirus H,Hepatovirus H, +Hepatovirus I,Hepatovirus I, +Hughes orthonairovirus,Hughes orthonairovirus, +Hunnivirus A,Hunnivirus A, +Imjin thottimvirus,Imjin thottimvirus, +Infectious bursal disease virus,Infectious bursal disease virus, +Infectious pancreatic necrosis virus,Infectious pancreatic necrosis virus, +Salmon isavirus,Salmon isavirus, +Influenza D virus,Influenza D virus, +Iranian wheat stripe tenuivirus,Iranian wheat stripe tenuivirus, +Iriri curiovirus,Iriri curiovirus, +Israel turkey meningoencephalomyelitis virus,Israel turkey meningoencephalomyelitis virus, +Itacaiunas curiovirus,Itacaiunas curiovirus, +Jeju orthohantavirus,Jeju orthohantavirus, +Jembrana disease virus,Jembrana disease virus, +Joinjakaka hapavirus,Joinjakaka hapavirus, +Kadam virus,Kadam virus, +Kadipiro virus,Kadipiro virus, +Thetaarterivirus kafuba,Thetaarterivirus kafuba, +Kamese hapavirus,Kamese hapavirus, +Kenkeme orthohantavirus,Kenkeme orthohantavirus, +Keterah orthonairovirus,Keterah orthonairovirus, +Kibale herbevirus,Kibale herbevirus, +Zetaarterivirus ugarco 1,Zetaarterivirus ugarco 1, +Etaarterivirus ugarco 1,Etaarterivirus ugarco 1, +Iotaarterivirus kibreg 1,Iotaarterivirus kibreg 1, +Klamath tupavirus,Klamath tupavirus, +Koala retrovirus,Koala retrovirus, +Koolpinyah ephemerovirus,Koolpinyah ephemerovirus, +Kumasi ledantevirus,Kumasi ledantevirus, +Kunsagivirus A,Kunsagivirus A, +La Joya hapavirus,La Joya hapavirus, +Laibin mobatvirus,Laibin mobatvirus, +Landjia hapavirus,Landjia hapavirus, +Le Dantec ledantevirus,Le Dantec ledantevirus, +Lettuce big-vein associated varicosavirus,Lettuce big-vein associated varicosavirus, +Liao ning virus,Liao ning virus, +Limnipivirus A,Limnipivirus A, +Limnipivirus B,Limnipivirus B, +Luxi orthohantavirus,Luxi orthohantavirus, +Maize rough dwarf virus,Maize rough dwarf virus, +Maize stripe tenuivirus,Maize stripe tenuivirus, +Mal de Rio Cuarto virus,Mal de Rio Cuarto virus, +Mamastrovirus 5,Mamastrovirus 5, +Mamastrovirus 8,Mamastrovirus 8, +Manitoba hapavirus,Manitoba hapavirus, +Maporal orthohantavirus,Maporal orthohantavirus, +Marco hapavirus,Marco hapavirus, +Meaban virus,Meaban virus, +Megrivirus A,Megrivirus A, +Micromonas pusilla reovirus,Micromonas pusilla reovirus, +Thetaarterivirus mikelba 1,Thetaarterivirus mikelba 1, +Miniopterus bat coronavirus 1,Miniopterus bat coronavirus 1, +Mink coronavirus 1,Mink coronavirus 1, +Montano orthohantavirus,Montano orthohantavirus, +Morreton vesiculovirus,Morreton vesiculovirus, +Mosavirus A,Mosavirus A, +Mosqueiro hapavirus,Mosqueiro hapavirus, +Mossuril hapavirus,Mossuril hapavirus, +Mycoreovirus 1,Mycoreovirus 1, +Mycoreovirus 3,Mycoreovirus 3, +Nairobi sheep disease orthonairovirus,Nairobi sheep disease orthonairovirus, +Nilaparvata lugens reovirus,Nilaparvata lugens reovirus, +Nishimuro ledantevirus,Nishimuro ledantevirus, +Nkolbisson ledantevirus,Nkolbisson ledantevirus, +Nova mobatvirus,Nova mobatvirus, +Okahandja mammarenavirus,Okahandja mammarenavirus, +Orchid fleck dichorhavirus,Orchid fleck dichorhavirus, +Ord River hapavirus,Ord River hapavirus, +Parechovirus C,Parechovirus C, +Parechovirus D,Parechovirus D, +Parry Creek hapavirus,Parry Creek hapavirus, +Pasivirus A,Pasivirus A, +Passeriform 1 orthobornavirus,Passeriform 1 orthobornavirus, +Passerivirus A,Passerivirus A, +Deltaarterivirus pejah,Iotaarterivirus pejah, +Pegivirus B,Pegivirus B, +Pegivirus D,Pegivirus D, +Pegivirus F,Pegivirus F, +Pegivirus G,Pegivirus G, +Pegivirus I,Pegivirus I, +Pegivirus J,Pegivirus J, +Pegivirus K,Pegivirus K, +Phasi Charoen-like phasivirus,Phasi Charoen-like phasivirus, +Piscine orthoreovirus,Piscine orthoreovirus, +Betaarterivirus suid 2,Betaarterivirus suid 2, +Potamipivirus A,Potamipivirus A, +Psittaciform 1 orthobornavirus,Psittaciform 1 orthobornavirus, +Psittaciform 2 orthobornavirus,Psittaciform 2 orthobornavirus, +Quezon mobatvirus,Quezon mobatvirus, +Rabbit picobirnavirus,,Abolished +Rabovirus A,Rabovirus A, +Radi vesiculovirus,Radi vesiculovirus, +Betaarterivirus chinrav 1,Betaarterivirus chinrav 1, +Reptilian orthoreovirus,Reptilian orthoreovirus, +Reticuloendotheliosis virus,Reticuloendotheliosis virus, +Rice black streaked dwarf virus,Rice black streaked dwarf virus, +Rice dwarf virus,Rice dwarf virus, +Rice gall dwarf virus,Rice gall dwarf virus, +Rice grassy stunt tenuivirus,Rice grassy stunt tenuivirus, +Rice hoja blanca tenuivirus,Rice hoja blanca tenuivirus, +Rice ragged stunt virus,Rice ragged stunt virus, +Rice stripe tenuivirus,Rice stripe tenuivirus, +Rochambeau curiovirus,Rochambeau curiovirus, +Rockport orthohantavirus,Rockport orthohantavirus, +Rosavirus A,Rosavirus A, +Rotavirus D,Rotavirus D, +Rotavirus F,Rotavirus F, +Rotavirus G,Rotavirus G, +Rotavirus I,Rotavirus I, +Sakhalin orthonairovirus,Sakhalin orthonairovirus, +Sangassou orthohantavirus,Sangassou orthohantavirus, +Sapelovirus B,Sapelovirus B, +Saumarez Reef virus,Saumarez Reef virus, +Sena Madureira sripuvirus,Sena Madureira sripuvirus, +Senecavirus A,Senecavirus A, +Insect shangavirus,Insect shangavirus, +Epsilonarterivirus hemcep,Epsilonarterivirus hemcep, +Solwezi mammarenavirus,Solwezi mammarenavirus, +Southern rice black-streaked dwarf virus,Southern rice black-streaked dwarf virus, +Sripur sripuvirus,Sripur sripuvirus, +St Croix River virus,St Croix River virus, +Strawberry crinkle cytorhabdovirus,Strawberry crinkle cytorhabdovirus, +Sweetwater Branch tibrovirus,Sweetwater Branch tibrovirus, +Tai herbevirus,Tai herbevirus, +Tellina virus,Tellina virus, +Tete orthobunyavirus,Tete orthobunyavirus, +Teviot pararubulavirus,Teviot pararubulavirus, +Thimiri orthobunyavirus,Thimiri orthobunyavirus, +Torchivirus A,Torchivirus A, +Umatilla virus,Umatilla virus, +Walleye dermal sarcoma virus,Walleye dermal sarcoma virus, +Waterbird 1 orthobornavirus,Waterbird 1 orthobornavirus, +Kappaarterivirus wobum,Kappaarterivirus wobum, +Wound tumor virus,Wound tumor virus, +Fly wubeivirus,Fly phasivirus, +Wuhan ledantevirus,Wuhan ledantevirus, +Wutai mosquito phasivirus,Wutai mosquito phasivirus, +Yaounde virus,Yaounde virus, +Yata ephemerovirus,Yata ephemerovirus, +Yellowtail ascites virus,Yellowtail ascites virus, +Yichang insect goukovirus,Yichang insect goukovirus, +Yongjia ledantevirus,Yongjia ledantevirus, +Yunnan orbivirus,Yunnan orbivirus, diff --git a/Makefile b/Makefile index 7fc92ab..aab5060 100644 --- a/Makefile +++ b/Makefile @@ -65,7 +65,7 @@ ExternalData/ICTV_MasterSpeciesList_2018b.xlsx: ExternalData/WoolhouseBrierley_2018.xlsx: mkdir -p ExternalData - curl -L -o $(@D)/WB2018.zip 'http://datashare.is.ed.ac.uk/download/DS_10283_2970.zip' + curl -k -L -o $(@D)/WB2018.zip 'https://datashare.is.ed.ac.uk/download/DS_10283_2970.zip' unzip -u -d $(@D) $(@D)/WB2018.zip 'Woolhouse and Brierley RNA virus database.xlsx' mv $(@D)/'Woolhouse and Brierley RNA virus database.xlsx' $(@D)/WoolhouseBrierley_2018.xlsx touch $(@D)/WoolhouseBrierley_2018.xlsx # Simply updates 'last modified' date, since unzip doesn't do this @@ -417,7 +417,6 @@ Plots/Figure1.pdf: CalculatedData/SplitData_Training.rds \ InternalData/Taxonomy_UnclassifiedViruses.csv \ RunData/TaxonomyHeuristic/Test_BootstrapPredictions.rds \ $(TRAIN_OUTPUT_FOLDERS) \ - RunData/AllGenomeFeatures_LongRun/AllGenomeFeatures_LongRun_Predictions.rds \ RunData/AllGenomeFeatures_LongRun/AllGenomeFeatures_LongRun_Bagged_predictions.rds Rscript Scripts/Plotting/MakeFigure1.R @@ -437,7 +436,7 @@ Plots/Figure3.pdf: RunData/AllGenomeFeatures_LongRun/AllGenomeFeatures_LongRun_B Plots/Figure1.pdf \ ExternalData/NovelViruses/ICTV_MasterSpeciesList_2019.v1.xlsx \ InternalData/NovelVirus_Hosts_Curated.csv \ - ExternalData/NovelViruses/NovelViruses.csv + ExternalData/NovelViruses/NovelViruses.gb Rscript Scripts/Plotting/MakeFigure3.R @@ -551,18 +550,20 @@ Plots/TableS1.csv: Plots/Figure3.pdf make_plots: Plots/Figure1.pdf \ Plots/Figure2.pdf \ Plots/Figure3.pdf \ + Plots/Figure4.pdf \ + Plots/Figure5.pdf \ Plots/Supplement_RawData.pdf \ Plots/Supplement_family_auc.pdf \ + Plots/Supplement_RelatednessModelRanks.pdf \ Plots/Supplement_TrainingSetRanks.pdf \ + Plots/Supplement_ScreeningSuccessRate.pdf \ Plots/Supplement_HighPriority_MissingZoonoses.pdf \ Plots/Supplement_bk_plots.pdf \ - Plots/Combine_tanglegrams.pdf \ Plots/SupplementaryFigure_FeatureClusters.pdf \ Plots/SupplementaryFigure_EffectDirection.pdf \ - Plots/Supplement_Sarbecovirus_ranks.pdf \ + Plots/Supplement_NovelVirus_Hosts.pdf \ Plots/Supplement_methods_derived_genome_features.pdf \ Plots/Supplement_FeatureSelection.pdf \ - Plots/Supplement_NovelVirus_Hosts.pdf \ Plots/TableS1.csv @@ -582,9 +583,10 @@ as_distributed: confirm -rm -rfv ExternalData -rm -rfv Plots -rm -rfv Predictions + -rm -rfv cached_blast_searches -rm -fv .Renviron - -find CalculatedData -maxdepth 1 -not -name CalculatedData -not -name GenomicFeatures-*.rds -not -name SplitData_Training.rds -delete - -find RunData -maxdepth 1 -not -name -not RunData -name AllGenomeFeatures_LongRun -not -name PN_LongRun -delete + -find CalculatedData -maxdepth 1 -not -name CalculatedData -not -name GenomicFeatures-*.rds -not -name SplitData_Training.rds -exec rm -rf {} \; + -find RunData -maxdepth 1 -not -name RunData -not -name AllGenomeFeatures_LongRun -not -name PN_LongRun -exec rm -rf {} \; -rm -fv RunData/AllGenomeFeatures_LongRun/AllGenomeFeatures_LongRun_Bagged_predictions.rds -rm -fv RunData/AllGenomeFeatures_LongRun/AllGenomeFeatures_LongRun_Bagging_AUCs.rds -rm -fv RunData/AllGenomeFeatures_LongRun/AllGenomeFeatures_LongRun_CalculatedData.rds diff --git a/README.md b/README.md index faeb64e..efb99c0 100644 --- a/README.md +++ b/README.md @@ -17,23 +17,33 @@ For a list of priority categories and ranks for all virus species in the paper, ## Requirements -- [R](https://www.r-project.org/) (tested using version 3.5.1) - - Most required R libraries can be installed using `Rscript -e "renv::restore()"` - - Install `ggtree` from bioconductor using: `Rscript -e "install.packages('BiocManager'); BiocManager::install('ggtree')"` -- [Python](https://www.python.org/) (version >=3.6) - - [Biopython](https://biopython.org/) - - [Pandas](https://pandas.pydata.org/) - - [xlrd](https://xlrd.readthedocs.io/en/latest/) -- [Java JDK](https://www.oracle.com/uk/java/technologies/javase-downloads.html) (version >=8) -If repeating all analyses (see below), the [BLAST+ suite of applications](https://www.ncbi.nlm.nih.gov/books/NBK279670/?report=classic) are also required (used for "phylogenetic neighbourhood" analyses and predictions, but not otherwise required). If your R session has trouble finding the BLAST+ executables, run `make update_path` and enter the location of the BLAST executables (e.g. `/usr/local/ncbi/blast/bin`). Making figure S9 requires [iqtree](http://www.iqtree.org/). +- Install the [conda package manager](https://conda.io/) +- Create the base environment +This installs everything required for prediction of new viruses +``` +conda env create -f base_environment.yml +``` + +- Before each use, activate this environment using +``` +conda activate zoonotic_rank +``` + +### Repeating published analyses +If repeating all analyses in the manuscript (see below), a few additional tools and R libraries are needed. The majority of these can be added to the base environment created above using: +``` +conda env update -n zoonotic_rank -f dev_environment.yml +``` + +The [BLAST+ suite of applications](https://www.ncbi.nlm.nih.gov/books/NBK279670/?report=classic) is also required (used for "phylogenetic neighbourhood" analyses and predictions). Version 2.8.1+ was used in the manuscript. If your R session has trouble finding the BLAST+ executables, run `make update_path` and enter the location of the BLAST executables (e.g. `/usr/local/ncbi/blast/bin`). ## Ranking novel viruses -Ranks for novel viruses can be generated by specifying the input format, paths to genome and metadata files, and a name for output files, e.g: +Ranks for novel viruses can be generated by specifying the input sequence format, paths to genome and metadata files, and a name for output files, e.g: ``` -Scripts/PredictNovel.R fasta \ +Rscript Scripts/PredictNovel.R fasta \ InternalData/example_files/genomes.fasta \ InternalData/example_files/metadata.csv \ example_1 @@ -41,7 +51,7 @@ Scripts/PredictNovel.R fasta \ For detailed instructions and further options, see ``` -Scripts/PredictNovel.R --help +Rscript Scripts/PredictNovel.R --help ``` #### Input @@ -79,10 +89,10 @@ File | Description Follow instructions below to repeat the analyses described in the manuscript. Note that these steps are _not_ needed to make predictions as described above (pre-trained models are included). Running all analyses takes ~3 weeks on a 4-core, 2.8 GHz i7 processor and requires ~5Gb of disk space. #### Basic -These steps will download any missing source data and automatically create/update files as needed. +These steps will download all external data and re-run the entire pipeline. _Using Rstudio:_ -1. Open `ZoonosisPredictor.Rproj` in RStudio +1. Open `zoonotic_rank.Rproj` in RStudio 2. On the `Build` tab, select `More` > `Clean and Rebuild` _Using the command-line:_ @@ -93,7 +103,6 @@ make clean all #### Advanced options (command-line only) - Use `make help` to see individual steps in the pipeline. Upstream steps are run automatically if needed. For example, using `make prepare` will run the data cleanup step, but also downloads the raw data if needed. -- `make ` runs all steps neccesary to produce/update the specified file (e.g. `make Plots/Figure1.pdf`). - `make as_distributed` resets the project to the state in which it was distributed. - `make clean` removes all run-related files, allowing a complete re-run (in contrast to `as_distributed`, this includes removing the pre-trained models required for prediction). @@ -103,50 +112,41 @@ make clean all ``` └─zoonotic_rank/ - ├─Makefile ................................. Record of workflow and dependencies - │ between files - ├─options.config ........................... Runtime options (speciefies number - │ of parrallel threads allowed and - │ the random seed) + ├─Makefile ................................. Record of workflow and dependencies between files + ├─options.config ........................... Runtime options (speciefies number of parrallel + │ threads allowed and the random seed) + ├─base_environment.yml ..................... Record of software and R libraries required for + │ prediction + ├─dev_environment.yml ...................... Record of additional software required to train and + │ evaulate models ├─InternalData/ ............................ All data unique to this project - │ ├─example_files/ ....................... Example input files for - │ │ predicting novel viruses - │ ├─Shaw2017_raw/ ........................ Raw ISG data from Shaw et al. - │ │ 2017 (see https://isg.data.cvr.ac.uk/) - │ ├─FinalData_Cleaned.csv .................Final dataset, as used for training. - │ │ Created by merging files below - │ │ (see Scripts/MergeAndCleanData.R) - │ ├─AllInternalData_Checked.csv .......... Metadata for the viruses used - │ │ as training data - │ ├─Final_Accessions_Unique_Spp.csv ...... Accession numbers of sequences - │ │ used for training (replaces - │ │ those in the metadata file) - │ ├─NameMatches_All.csv .................. Manually curated list used to - │ │ match virus names to unique - │ │ species across external datasets - │ ├─SourcesOfZoonoses_BabayanZoonotic.csv Additional zoonotic status data - │ │ for species not available in - │ │ external data sources - │ └─Taxonomy_UnclassifiedViruses.csv ..... Taxonomic information for - │ unclassified viruses in the - │ metadata (unused) + │ ├─example_files/ ....................... Example input files for predicting novel viruses + │ ├─Shaw2017_raw/ ........................ Raw ISG data from Shaw et al. 2017 + │ │ (see https://isg.data.cvr.ac.uk/) + │ ├─FinalData_Cleaned.csv .................Final dataset, as used for training. Created by + │ │ merging files below (Scripts/MergeAndCleanData.R) + │ ├─AllInternalData_Checked.csv .......... Metadata for the viruses used as training data + │ ├─Final_Accessions_Unique_Spp.csv ...... Accession numbers of sequences used for training + │ │ (replaces those in the metadata file) + │ ├─NameMatches_All.csv .................. Manually curated list used to match virus names to + │ │ unique species across external datasets + │ ├─SourcesOfZoonoses_BabayanZoonotic.csv Additional zoonotic status data for species not + │ │ available in external data sources + │ └─Taxonomy_UnclassifiedViruses.csv ..... Taxonomic information for unclassified viruses in + │ the metadata (unused) │ - ├─CalculatedData/ .......................... Intermediate calculations ([*], except - │ for files required by PredictNovel.R) - ├─ExternalData/ ............................ [*] Data from external sources, - │ dowloaded as needed (see Makefile) - ├─Misc/ .................................... Miscelaneous scripts to download - │ external data + ├─CalculatedData/ .......................... Intermediate calculations ([*], except for files + │ required by PredictNovel.R) + ├─ExternalData/ ............................ [*] Data from external sources, dowloaded as needed + │ (see Makefile) + ├─Misc/ .................................... Miscelaneous scripts to download external data ├─Plots/ ................................... [*] Final plots generated ├─Predictions/ ............................. [*] Predictions for case studies - ├─renv/ .................................... Record of R libraries required - ├─RunData/ ................................. Trained models ([*], except for - │ files required by PredictNovel.R) - ├─Scripts/ ................................. Main analysis, prediction, and - │ │ plotting scripts + ├─RunData/ ................................. Trained models ([*], except for files required + │ by PredictNovel.R) + ├─Scripts/ ................................. Main analysis, prediction, and plotting scripts │ └─Plotting/ ............................ Scripts to generate published plots - ├─Tests/ ................................... Unit tests for basic functionality - │ of utility scripts - └─Utils/ ................................... Utility functions and tools called - by other scripts + ├─Tests/ ................................... Unit tests for basic functionality of utility + │ functions/scripts + └─Utils/ ................................... Utility functions and tools called by other scripts ``` diff --git a/Scripts/CalculateBaggedPredictions.R b/Scripts/CalculateBaggedPredictions.R index 4a31bbf..2b7e4fe 100644 --- a/Scripts/CalculateBaggedPredictions.R +++ b/Scripts/CalculateBaggedPredictions.R @@ -38,7 +38,6 @@ library(rprojroot) library(dplyr) library(tidyr) library(ModelMetrics) -library(betacal) library(parallel) diff --git a/Scripts/Plotting/MakeSupplement_FeatureSelection.R b/Scripts/Plotting/MakeSupplement_FeatureSelection.R index 3d32881..b39110a 100644 --- a/Scripts/Plotting/MakeSupplement_FeatureSelection.R +++ b/Scripts/Plotting/MakeSupplement_FeatureSelection.R @@ -6,7 +6,6 @@ library(dplyr) library(tidyr) library(readr) library(ModelMetrics) -library(plotly) source(file.path('Scripts', 'Plotting', 'PlottingConstants.R')) source(file.path('Utils', 'rundata_utils.R')) diff --git a/Scripts/Plotting/MakeSupplement_HumanGeneSetSimilarity.R b/Scripts/Plotting/MakeSupplement_HumanGeneSetSimilarity.R deleted file mode 100644 index 265ceaf..0000000 --- a/Scripts/Plotting/MakeSupplement_HumanGeneSetSimilarity.R +++ /dev/null @@ -1,126 +0,0 @@ -library(dplyr) -library(ggplot2) -library(cowplot) -library(doParallel) -library(caret) -# library(pheatmap) -# library(scales) - -source(file.path('Scripts', 'Plotting', 'PlottingConstants.R')) - -gene_set_colours <- c('Housekeeping' = FEATURE_SET_COLOURS[['Housekeeping gene mimicry']], - 'ISG' = FEATURE_SET_COLOURS[['ISG mimicry']], - 'Remaining' = FEATURE_SET_COLOURS[['Remaining gene mimicry']]) - -## Data -human_gene_features <- readRDS('CalculatedData/GenomicFeatures-HumanCombined.rds') - - -# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -# ---- Heatmap ------------------------------------------------------------------------------------ -# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -# NOTE: This figure is unused - across all features, we expect genes to cluster by their ancestral -# relationships, but this does not mean they are not distinguishable on the basis of a few -# features which may have changed because of their role/when they are expressed - -# gene_sets <- human_gene_features %>% -# select(.data$GeneID, .data$GeneSet) -# -# stopifnot(length(unique(gene_sets$GeneID)) == nrow(gene_sets)) # Expect rows to be individual genes -# -# -# # Create a matrix of feature values for each gene -# feature_mat <- human_gene_features %>% -# select(-GeneID, -meanCPM, -TranscriptID, -GeneSet) %>% -# as.matrix() %>% -# t() -# -# colnames(feature_mat) <- human_gene_features$GeneID -# -# # Remove genes with only NA values -# all_na <- apply(feature_mat, 2, function(col) all(is.na(col))) -# message('Removing ', sum(all_na), ' genes with no feature values') -# -# feature_mat <- feature_mat[, !all_na] -# -# -# # Scale all features to [0-1], so no feature dominates clustering, and all rows are directly comparable -# # - Note: this also transposes the matrix, but that is needed anyway since we have more vertical -# # than horizontal space (so putting genes on y axis) -# scaled_feature_mat <- apply(feature_mat, MARGIN = 1, FUN = rescale) -# rownames(scaled_feature_mat) <- colnames(feature_mat) -# -# # Plot -# row_annotations <- data.frame(Set = gene_sets$GeneSet) -# rownames(row_annotations) <- gene_sets$GeneID -# -# pheatmap(scaled_feature_mat, annotation_row = row_annotations, -# annotation_colors = list(Set = gene_set_colours), -# show_rownames = FALSE, show_colnames = FALSE, -# annotation_names_col = FALSE, -# filename = file.path('Plots', 'Supplement_HumanGeneSetSimilarity_Heatmap.pdf')) - - - -# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -# ---- Predictions -------------------------------------------------------------------------------- -# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -# Train a classifier to see whether the sets of genes can be distinguished based on their -# genome features -cl <- makeCluster(8) -registerDoParallel(cl) - -train_data <- human_gene_features %>% - select(-GeneID, -meanCPM, -TranscriptID) - - -trainSettings <- trainControl(method = 'repeatedcv', - number = 10, - repeats = 3, - search = 'random', - returnResamp = 'all', - sampling = 'down', - savePredictions = 'final', - classProbs = TRUE, - summaryFunction = mnLogLoss) - -trainedModel <- train(GeneSet ~ ., - data = train_data, - method = 'xgbTree', # Also try xgbDART and xgbTree - trControl = trainSettings, - metric = 'logLoss', - tuneLength = 100, - na.action = 'na.pass', - nthread = 1) - - -# Plot accuracy across CV folds -final_preds <- trainedModel$pred %>% - group_by(.data$obs, .data$Resample) %>% - mutate(obs_class_size = n()) %>% - group_by(.data$obs, .data$pred, .data$Resample) %>% - summarise(Proportion = n()/unique(.data$obs_class_size)) - - -preds_plot <- ggplot(final_preds, aes(x = obs, y = Proportion, colour = pred)) + - geom_boxplot() + - scale_colour_manual(values = gene_set_colours) + - labs(x = 'Actual class', y = 'Proportion of actual class', colour = 'Predicted class') + - PLOT_THEME - - - -registerDoSEQ() -stopCluster(cl) - - -# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -# ---- Output ------------------------------------------------------------------------------------- -# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -# Save trained model -saveRDS(trainedModel, - file.path('Plots', 'Intermediates', 'Supplement_HumanGeneSetSimilarity_trainedmodel_xgbTree.rds')) - - -# Save plot -ggsave2(file.path('Plots', 'Supplement_HumanGeneSetSimilarity_xgbTree.pdf'), preds_plot, width = 7, height = 4) diff --git a/Scripts/Plotting/MakeSupplementaryFigure_EffectDirection.R b/Scripts/Plotting/MakeSupplementaryFigure_EffectDirection.R index c528e84..228e078 100644 --- a/Scripts/Plotting/MakeSupplementaryFigure_EffectDirection.R +++ b/Scripts/Plotting/MakeSupplementaryFigure_EffectDirection.R @@ -3,7 +3,9 @@ ## library(scales) -library(tidyverse) +library(dplyr) +library(tidyr) +library(stringr) library(apcluster) library(cowplot) library(ggbeeswarm) diff --git a/Scripts/Plotting/MakeSupplementaryFigure_FeatureClusters.R b/Scripts/Plotting/MakeSupplementaryFigure_FeatureClusters.R index 56d3537..008fd8e 100644 --- a/Scripts/Plotting/MakeSupplementaryFigure_FeatureClusters.R +++ b/Scripts/Plotting/MakeSupplementaryFigure_FeatureClusters.R @@ -3,7 +3,9 @@ ## set.seed(1521312) -library(tidyverse) +library(dplyr) +library(tidyr) +library(stringr) library(cowplot) library(apcluster) diff --git a/Scripts/Plotting/PlottingConstants.R b/Scripts/Plotting/PlottingConstants.R index b571f8d..3ff8cc7 100644 --- a/Scripts/Plotting/PlottingConstants.R +++ b/Scripts/Plotting/PlottingConstants.R @@ -2,8 +2,15 @@ ## General plot settings, used to ensure consistency between plots ## ================================================================================================= +# Not available on conda, but exact version does not matter anyway +suppressPackageStartupMessages({ + if (!require("khroma")) { + install.packages("khroma", repos = "https://cloud.r-project.org", verbose = FALSE) + library(khroma) + } +}) + library(ggplot2) -library(khroma) library(colorspace) # Overall theme diff --git a/Scripts/Plotting/Supplement_TopFeatures_ComparedToHumanValues.R b/Scripts/Plotting/Supplement_TopFeatures_ComparedToHumanValues.R deleted file mode 100644 index 4deca7f..0000000 --- a/Scripts/Plotting/Supplement_TopFeatures_ComparedToHumanValues.R +++ /dev/null @@ -1,11 +0,0 @@ -# -# Plot the distributions of the most predictive features in the underlying human genes -# - Trying to illustrate mimicry in a more visual / intuitive way -# - -library(dplyr) -library(tidyr) -library(stringr) -library(ggplot2) - -source(file.path('Scripts', 'Plotting', 'PlottingConstants.R')) \ No newline at end of file diff --git a/Scripts/PredictNovel.R b/Scripts/PredictNovel.R old mode 100755 new mode 100644 index 21799be..a15c733 --- a/Scripts/PredictNovel.R +++ b/Scripts/PredictNovel.R @@ -100,7 +100,6 @@ suppressPackageStartupMessages({ library(ModelMetrics) library(apcluster) library(ape) - library(betacal) library(EnvStats) }) diff --git a/Scripts/PredictNovel_PN.R b/Scripts/PredictNovel_PN.R index 65c2f2a..a97bb4b 100644 --- a/Scripts/PredictNovel_PN.R +++ b/Scripts/PredictNovel_PN.R @@ -85,7 +85,6 @@ suppressPackageStartupMessages({ library(ModelMetrics) library(apcluster) library(ape) - library(betacal) }) diff --git a/Scripts/TrainFamilyHeuristic.R b/Scripts/TrainFamilyHeuristic.R index 1fe4f49..4675e7f 100644 --- a/Scripts/TrainFamilyHeuristic.R +++ b/Scripts/TrainFamilyHeuristic.R @@ -51,7 +51,10 @@ CV_K <- 5 # Number of folds for k-fold cross-validation # ---- Data --------------------------------------------------------------------------------------- # =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= library(parallel) -library(tidyverse) +library(dplyr) +library(tidyr) +library(readr) +library(stringr) library(readxl) library(ModelMetrics) library(caret) diff --git a/Utils/PNsummary_utils.R b/Utils/PNsummary_utils.R index 6538d97..443e332 100644 --- a/Utils/PNsummary_utils.R +++ b/Utils/PNsummary_utils.R @@ -8,7 +8,6 @@ library(ape) library(dplyr) library(tidyr) library(parallel) -library(rdiversity) ROOT_DIR <- find_rstudio_root_file() @@ -52,6 +51,8 @@ add_names_to_blast <- function(blastRes, data) { # # returns: a data frame with columns 'Neighbourhood' and 'Diversity' calculate_diversity <- function(observations, neighbourhoodIDs, phylo) { + require(rdiversity) + # Check input if (length(observations) != length(neighbourhoodIDs)) stop('observations and neighbourhoodIDs should have equal length') diff --git a/Utils/calibration_utils.R b/Utils/calibration_utils.R index 91d12d8..6d4f8a7 100644 --- a/Utils/calibration_utils.R +++ b/Utils/calibration_utils.R @@ -1,5 +1,12 @@ # Zoonosis predictor: Utility functions to calibrate predictions -require(betacal) + +# betacal can't be installed via conda: +suppressPackageStartupMessages({ + if (!require("betacal")) { + install.packages("betacal", repos = "https://cloud.r-project.org", verbose = FALSE) + library(betacal) + } +}) calibrate_preds <- function(predictions, calibration_preds, positive_name = 'True') { # 'predictions': a data frame of predictions requiring calibration diff --git a/base_environment.yml b/base_environment.yml new file mode 100644 index 0000000..d6815f1 --- /dev/null +++ b/base_environment.yml @@ -0,0 +1,27 @@ +name: zoonotic_rank + +channels: + - conda-forge + +dependencies: + - r-base=3.5.1 + - r-argparse=2.0.1 + - r-rprojroot=1.3_2 + - r-seqinr=3.4 + - r-dplyr=0.8.3 + - r-tidyr=0.8.3 + - r-stringr=1.4.0 + - r-readr=1.3.1 + - r-ggplot2=3.2.0 + - r-xgboost=0.90 + - r-caret=6.0_85 + - r-modelmetrics=1.2 + - r-apcluster=1.4.8 + - r-ape=5.1 + - r-envstats=2.3.1 + - python=3.6.5 + - biopython=1.72 + - xlrd=1.1.0 + - pandas=0.23.0 + - requests=2.18.4 + - openjdk=11.0.1 diff --git a/dev_environment.yml b/dev_environment.yml new file mode 100644 index 0000000..a38543e --- /dev/null +++ b/dev_environment.yml @@ -0,0 +1,30 @@ +channels: + - conda-forge + - bioconda + - defaults + +dependencies: + - r-base=3.5.1 + - iqtree=2.0.3 + - r-readxl=1.3.1 + - r-purrr=0.3.2 + - r-rjson=0.2.20 + - r-matrixstats=0.54 + - r-doparallel=1.0.14 + - r-plyr=1.8.4 + - r-e1071=1.7_0 + - r-digest=0.6.15 + - r-cowplot=1.0.0 + - r-ggsignif=0.6.0 + - r-plotroc=2.2.1 + - r-scales=1.1.0 + - r-colorspace=1.4_1 + - r-cluster=2.1.0 + - r-egg=0.4.5 + - bioconductor-ggtree=1.14.6 + - 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