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.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

phastest-compare.R

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+library('ggplot2')
+library('tidyverse')
+library('paletteer')
+library('dplyr')
+library('jsonlite')
+#####Setup######
+BAproph <- fromJSON("PHASTEST/Banthracis.PHASTEST/predicted_genes.json", flatten=TRUE)
+BAproph<-BAproph%>%
+  mutate(genus=('Bacillus'),species=('anthracis'),.before=index)
+
+BCproph <- fromJSON("PHASTEST/Bcereus.PHASTEST/predicted_genes.json", flatten=TRUE)
+BCproph<-BCproph%>%
+  mutate(genus=('Bacillus'),species=('cereus'),.before=index)
+
+BTproph <- fromJSON("PHASTEST/Bthuringiensis.PHASTEST/predicted_genes.json", flatten=TRUE)
+BTproph<-BTproph%>%
+  mutate(genus=('Bacillus'),species=('thuringiensis'),.before=index)
+
+BLproph <- fromJSON("PHASTEST/Blicheniformis.PHASTEST/predicted_genes.json", flatten=TRUE)
+BLproph<-BLproph%>%
+  mutate(genus=('Bacillus'),species=('licheniformis'),.before=index)
+
+CBproph <- fromJSON("PHASTEST/Cbotulinum.PHASTEST/predicted_genes.json", flatten=TRUE)
+CBproph<-CBproph%>%
+  mutate(genus=('Clostridium'),species=('botulinum'),.before=index)
+
+CDproph <- fromJSON("PHASTEST/Cdifficile.PHASTEST/predicted_genes.json", flatten=TRUE)
+CDproph<-CDproph%>%
+  mutate(genus=('Clostridium'),species=('difficile'),.before=index)
+
+CPproph <- fromJSON("PHASTEST/Cperf.PHASTEST/predicted_genes.json", flatten=TRUE)
+CPproph<-CPproph%>%
+  mutate(genus=('Clostridium'),species=('perfringens'),.before=index)
+
+CTproph <- fromJSON("PHASTEST/Ctetani.PHASTEST/predicted_genes.json", flatten=TRUE)
+CTproph<-CTproph%>%
+  mutate(genus=('Clostridium'),species=('tetani'),.before=index)
+
+#combine the data frames for each organism
+phage<-rbind(CTproph,CPproph,CDproph,CBproph,BLproph,BAproph,BTproph,BCproph)
+
+#rm rows for genes not in a prophage region
+phage <- phage[phage$region_index != "Bacterial", ]
+
+#create objects
+genus=phage$genus
+species=phage$species
+type=phage$type
+
+
+####Add Groups ######
+
+phage$Org <- case_when(
+  species == "anthracis"~"B. anthracis",
+  species == "cereus"~"B. cereus",
+  species == "licheniformis"~"B. licheniformis",
+  species == "thuringiensis"~"B. thuringiensis",
+  species == "botulinum"~"C. botulinum",
+  species == "difficile"~"C. difficile",
+  species == "perfringens"~"C. perfringens",
+  species == "tetani"~"C. tetani",
+  .default = as.character(species)
+)
+phage$Type <- case_when(
+  type == "Attachment_site"~"Attachment site",
+  type == "Fiber_protein"~"Virion",
+  type == "Head_protein"~"Virion",
+  type == "Hypothetical_protein"~"Hypothetical",
+  type == "Non_phage-like_protein"~"Bacterial",
+  type == "Phage-like_protein"~"Phage-like",
+  type == "Plate_protein"~"Virion",
+  type == "Portal_protein"~"Virion",
+  type == "Tail_protein"~"Virion",
+  type == "Terminase"~"Other",
+  type == "Protease"~"Other",
+  type == "Transposase"~"Other",
+  type == "tRNA"~"Other",
+  type == "Integrase"~"Other",
+  type == "Protease"~"Other",
+  type == "Lysis_protein"~"Other",
+  type == "Antirepressor"~"Other",
+  type == "Crossover_junction_protein"~"Other",
+  type == "Endodeoxyribonuclease"~"Other",
+  type == "Endonuclease"~"Other",
+  type == "Holin"~"Other",
+  type == "Integrase"~"Other",
+  type == "Membrane_protein"~"Other",
+  type == "Neck_protein"~"Virion",
+  type == "phage antirepressor KilAC domain-containing protein"~"Other",
+  type == "phage DNA-binding protein"~"Other",
+  type == "phage exported protein"~"Other",
+  type == "phage family Tn916-like,CTn6-Orf1"~"Other",
+  type == "phage holin family protein"~"Other",
+  type == "phage infection protein"~"Other",
+  type == "phage integrase"~"Other",
+  type == "phage major capsid protein"~"Virion",
+  type == "phage packaging/lysis transcriptional regulator"~"Other",
+  type == "phage portal protein"~"Virion",
+  type == "phage protein"~"Other",
+  type == "phage protein (partial)"~"Other",
+  type == "phage RecT protein"~"Other",
+  type == "phage related N-acetylmuramoyl-L-alanine amidase"~"Other",
+  type == "phage related protein"~"Other",
+  type == "phage replication protein"~"Other",
+  type == "phage repressor protein"~"Other",
+  type == "phage shock protein"~"Other",
+  type == "phage shock protein (rhodanese)"~"Other",
+  type == "phage surface protein"~"Other",
+  type == "phage tail spike protein"~"Virion",
+  type == "phage terminase small subunit"~"Other",
+  type == "phage tyrosine recombinase"~"Other",
+  type == "phage-like protein"~"Phage-like",
+  type == "phage-related cell wall hydrolase"~"Other",
+  type == "phage-related deoxyuridylate hydroxymethyltransferase"~"Other",
+  type == "phage-related protein"~"Phage-like",
+  type == "phage-related repressor"~"Other",
+  type == "phage-related single-strand DNA binding protein"~"Other",
+  type == "phage-type"~"Other",
+  type == "Regulatory_protein"~"Other",
+  type == "Repressor"~"Other",
+  type == "Replication_protein"~"Other",
+  .default = as.character(type)
+)
+
+
+#####Plot#####
+cbPalette <- c("#018EF9", "#F76902", "#74B944","#D62728FF","#F6BE00", "#9467BDFF", "#A3D4D4","#DB4A72")
+
+ggplot(phage, aes(fill=Type, x=Org)) + 
+  geom_bar() +
+  ylab("Number of predicted genes") +xlab("Species") +
+  scale_x_discrete(guide = guide_axis(n.dodge = 2)) +
+  theme(axis.text.x= element_text(face="italic")) +
+  scale_y_continuous(expand = expansion(mult = c(0, 0.025))) +
+  scale_fill_manual(values=cbPalette)

phastest-compare.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX