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.Rhistory
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library(diagram)
openplotmat()
par(mar = c(2, 2, 2, 2))
openplotmat(main = paste("Sulfur Cycle:", name.of.genome)) # Add a title
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
elpos
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = input[23,2]) #S-S-01:Sulfide oxidation
read.csv("~/Desktop/Total.R_input.txt")
read.csv("~/Desktop/Total.R_input.txt", sep=)
read.csv("~/Desktop/Total.R_input.txt", sep="\t")
input <- read.table("~/Desktop/Total.R_input.txt", sep="\t")
library(diagram)
openplotmat()
par(mar = c(2, 2, 2, 2))
openplotmat(main = paste("Sulfur Cycle:", name.of.genome)) # Add a title
name.of.genome <- "test"
openplotmat(main = paste("Sulfur Cycle:", name.of.genome)) # Add a title
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
elpos
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = input[23,2]) #S-S-01:Sulfide oxidation
straightarrow(from = elpos[4, ], to = elpos[1, ], lty = 1, lcol = input[24,2]) #S-S-02:Sulfur reduction
straightarrow(from = elpos[4, ], to = elpos[10, ], lty = 1, lcol = input[25,2]) #S-S-03:Sulfur oxidation
straightarrow(from = elpos[10, ], to = elpos[11, ], lty = 1, lcol = input[26,2]) #S-S-04:Sulfite oxidation
straightarrow(from = elpos[11, ], to = elpos[5, ], lty = 1, lcol = input[27,2]) #S-S-05:Sulfate reduction
straightarrow(from = elpos[5, ], to = elpos[1, ], lty = 1, lcol = input[28,2]) #S-S-06:Sulfite reduction
straightarrow(from = elpos[6, ], to = elpos[11, ], lty = 1, lcol = input[29,2]) #S-S-07:Thiosulfate oxidation
splitarrow(from = elpos[6, ], to = elpos[c(1,10), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = input[30,2]) #S-S-08:Thiosulfate disproportionation
splitarrow(from = elpos[6, ], to = elpos[c(4,11), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = input[31,2]) #S-S-09:Thiosulfate disproportionation 2
View(input)
textrect (elpos[1, ], 0.07, 0.05, lab = expression(paste(H['2'],S,' ',(-2))), cex = 1.5)
textrect (elpos[4, ], 0.05, 0.05, lab = expression(paste(S,' ',(0))), cex = 1.5)
textrect (elpos[5, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[6, ], 0.07, 0.05, lab = expression(paste(S['2']*O['3'])^'2-'* ' '(+2)), cex = 1.5)
textrect (elpos[10, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[11, ], 0.07, 0.05, lab = expression(paste(SO['4'])^'2-'*' '(+6)), cex = 1.5)
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = input[23,2]) #S-S-01:Sulfide oxidation
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation"))
textplain(mid = c(0.68, 0.69),
lab = c("Step2: Sulfur reduction"))
textplain(mid = c(0.93, 0.5),
lab = c("Step3: Sulfur oxidation"))
textplain(mid = c(0.75, 0.15),
lab = c("Step4: Sulfite oxidation"))
textplain(mid = c(0.25, 0.23),
lab = c("Step5: Sulfate reduction"))
textplain(mid = c(0.23, 0.75),
lab = c("Step6: Sulfite reduction"))
textplain(mid = c(0.605, 0.32),
lab = c("Step7: Thiosulfate oxidation"))
textplain(mid = c(0.45, 0.61),
lab = c("Step8: Thiosulfate disproportionation 1"))
textplain(mid = c(0.45, 0.61),
lab = c("Step8: Thiosulfate disproportionation 2"))
textplain(mid = c(0.68, 0.61),
lab = c("Step8: Thiosulfate disproportionation 2"))
textplain(mid = c(0.68, 0.40),
lab = c("Step8: Thiosulfate disproportionation 2"))
openplotmat()
par(mar = c(2, 2, 2, 2))
openplotmat(main = "Sulfur Cycle : Summary Figure") # Add a tiitle
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = 1) #S-S-01:Sulfide oxidation
straightarrow(from = elpos[4, ], to = elpos[1, ], lty = 1, lcol = 1) #S-S-02:Sulfur reduction
straightarrow(from = elpos[4, ], to = elpos[10, ], lty = 1, lcol = 1) #S-S-03:Sulfur oxidation
straightarrow(from = elpos[10, ], to = elpos[11, ], lty = 1, lcol = 1) #S-S-04:Sulfite oxidation
straightarrow(from = elpos[11, ], to = elpos[5, ], lty = 1, lcol = 1) #S-S-05:Sulfate reduction
straightarrow(from = elpos[5, ], to = elpos[1, ], lty = 1, lcol = 1) #S-S-06:Sulfite reduction
straightarrow(from = elpos[6, ], to = elpos[11, ], lty = 1, lcol = 1) #S-S-07:Thiosulfate oxidation
splitarrow(from = elpos[6, ], to = elpos[c(1,10), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = 1) #S-S-08:Thiosulfate disproportionation 1
splitarrow(from = elpos[6, ], to = elpos[c(4,11), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = 1) #S-S-09:Thiosulfate disproportionation 2
textrect (elpos[1, ], 0.07, 0.05, lab = expression(paste(H['2'],S,' ',(-2))), cex = 1.5)
textrect (elpos[4, ], 0.05, 0.05, lab = expression(paste(S,' ',(0))), cex = 1.5)
textrect (elpos[5, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[6, ], 0.07, 0.05, lab = expression(paste(S['2']*O['3'])^'2-'* ' '(+2)), cex = 1.5)
textrect (elpos[10, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[11, ], 0.07, 0.05, lab = expression(paste(SO['4'])^'2-'*' '(+6)), cex = 1.5)
par(lheight=0.01)
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation",
paste("Genomes:",input.total$Nb.Genome[23]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[23],"%")))
input.total <- input.total
input.total <- input
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation",
paste("Genomes:",input.total$Nb.Genome[23]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[23],"%")))
View(input.total)
colnames(input.total) <- c("Reaction","Nb.Genome","Genome.Coverage.Percentages.Round")
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation",
paste("Genomes:",input.total$Nb.Genome[23]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[23],"%")))
openplotmat()
par(mar = c(2, 2, 2, 2))
openplotmat(main = "Sulfur Cycle : Summary Figure") # Add a tiitle
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = 1) #S-S-01:Sulfide oxidation
straightarrow(from = elpos[4, ], to = elpos[1, ], lty = 1, lcol = 1) #S-S-02:Sulfur reduction
straightarrow(from = elpos[4, ], to = elpos[10, ], lty = 1, lcol = 1) #S-S-03:Sulfur oxidation
straightarrow(from = elpos[10, ], to = elpos[11, ], lty = 1, lcol = 1) #S-S-04:Sulfite oxidation
straightarrow(from = elpos[11, ], to = elpos[5, ], lty = 1, lcol = 1) #S-S-05:Sulfate reduction
straightarrow(from = elpos[5, ], to = elpos[1, ], lty = 1, lcol = 1) #S-S-06:Sulfite reduction
straightarrow(from = elpos[6, ], to = elpos[11, ], lty = 1, lcol = 1) #S-S-07:Thiosulfate oxidation
splitarrow(from = elpos[6, ], to = elpos[c(1,10), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = 1) #S-S-08:Thiosulfate disproportionation 1
splitarrow(from = elpos[6, ], to = elpos[c(4,11), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = 1) #S-S-09:Thiosulfate disproportionation 2
textrect (elpos[1, ], 0.07, 0.05, lab = expression(paste(H['2'],S,' ',(-2))), cex = 1.5)
textrect (elpos[4, ], 0.05, 0.05, lab = expression(paste(S,' ',(0))), cex = 1.5)
textrect (elpos[5, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[6, ], 0.07, 0.05, lab = expression(paste(S['2']*O['3'])^'2-'* ' '(+2)), cex = 1.5)
textrect (elpos[10, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[11, ], 0.07, 0.05, lab = expression(paste(SO['4'])^'2-'*' '(+6)), cex = 1.5)
par(lheight=0.01)
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation",
paste("Genomes:",input.total$Nb.Genome[23]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[23],"%")))
colnames(input.total) <- c("Reaction","Nb.Genome","Genome.Coverage.Percentages")
input.total$Genome.Coverage.Percentages.Round <- round(input.total$Genome.Coverage.Percentages, digits=2)
View(input.total)
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation",
paste("Genomes:",input.total$Nb.Genome[23]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[23],"%")))
textplain(mid = c(0.68, 0.68),
lab = c("Step2: Sulfur reduction",
paste("Genomes:",input.total$Nb.Genome[24]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[24],"%")))
textplain(mid = c(0.93, 0.5),
lab = c("Step3: Sulfur",
"oxidation",
paste("Genomes:",input.total$Nb.Genome[25]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[25],"%")))
textplain(mid = c(0.75, 0.12),
lab = c("Step4: Sulfite oxidation",
paste("Genomes:",input.total$Nb.Genome[26]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[26],"%")))
textplain(mid = c(0.25, 0.20),
lab = c("Step5: Sulfate reduction",
paste("Genomes:",input.total$Nb.Genome[27]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[27],"%")))
textplain(mid = c(0.23, 0.75),
lab = c("Step6: Sulfite reduction",
paste("Genomes:",input.total$Nb.Genome[28]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[28],"%")))
textplain(mid = c(0.61, 0.32),
lab = c("Step7: Thiosulfate oxidation",
paste("Genomes:",input.total$Nb.Genome[29]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[29],"%")))
textplain(mid = c(0.45, 0.62),
lab = c("Step8: Thiosulfate disproportionation 1",
paste("Genomes:",input.total$Nb.Genome[30]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[30],"%")))
textplain(mid = c(0.68, 0.40),
lab = c("Step9: Thiosulfate disproportionation 2",
paste("Genomes:",input.total$Nb.Genome[31]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[31],"%")))
textplain(mid = c(0.51, 0.32),
lab = c("Step7: Thiosulfate oxidation",
paste("Genomes:",input.total$Nb.Genome[29]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[29],"%")))
textplain(mid = c(0.41, 0.32),
lab = c("Step7: Thiosulfate oxidation",
paste("Genomes:",input.total$Nb.Genome[29]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[29],"%")))
textplain(mid = c(0.41, 0.35),
lab = c("Step7: Thiosulfate oxidation",
paste("Genomes:",input.total$Nb.Genome[29]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[29],"%")))
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = 1) #S-S-01:Sulfide oxidation
straightarrow(from = elpos[4, ], to = elpos[1, ], lty = 1, lcol = 1) #S-S-02:Sulfur reduction
straightarrow(from = elpos[4, ], to = elpos[10, ], lty = 1, lcol = 1) #S-S-03:Sulfur oxidation
straightarrow(from = elpos[10, ], to = elpos[11, ], lty = 1, lcol = 1) #S-S-04:Sulfite oxidation
straightarrow(from = elpos[11, ], to = elpos[5, ], lty = 1, lcol = 1) #S-S-05:Sulfate reduction
openplotmat()
par(mar = c(2, 2, 2, 2))
openplotmat(main = "Sulfur Cycle : Summary Figure") # Add a tiitle
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = 1) #S-S-01:Sulfide oxidation
straightarrow(from = elpos[4, ], to = elpos[1, ], lty = 1, lcol = 1) #S-S-02:Sulfur reduction
straightarrow(from = elpos[4, ], to = elpos[10, ], lty = 1, lcol = 1) #S-S-03:Sulfur oxidation
straightarrow(from = elpos[10, ], to = elpos[11, ], lty = 1, lcol = 1) #S-S-04:Sulfite oxidation
straightarrow(from = elpos[11, ], to = elpos[5, ], lty = 1, lcol = 1) #S-S-05:Sulfate reduction
straightarrow(from = elpos[5, ], to = elpos[1, ], lty = 1, lcol = 1) #S-S-06:Sulfite reduction
straightarrow(from = elpos[6, ], to = elpos[11, ], lty = 1, lcol = 1) #S-S-07:Thiosulfate oxidation
splitarrow(from = elpos[6, ], to = elpos[c(1,10), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = 1) #S-S-08:Thiosulfate disproportionation 1
splitarrow(from = elpos[6, ], to = elpos[c(4,11), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = 1) #S-S-09:Thiosulfate disproportionation 2
textrect (elpos[1, ], 0.07, 0.05, lab = expression(paste(H['2'],S,' ',(-2))), cex = 1.5)
textrect (elpos[4, ], 0.05, 0.05, lab = expression(paste(S,' ',(0))), cex = 1.5)
textrect (elpos[5, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[6, ], 0.07, 0.05, lab = expression(paste(S['2']*O['3'])^'2-'* ' '(+2)), cex = 1.5)
textrect (elpos[10, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[11, ], 0.07, 0.05, lab = expression(paste(SO['4'])^'2-'*' '(+6)), cex = 1.5)
par(lheight=0.01)
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation",
paste("Genomes:",input.total$Nb.Genome[23]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[23],"%")))
textplain(mid = c(0.68, 0.68),
lab = c("Step2: Sulfur reduction",
paste("Genomes:",input.total$Nb.Genome[24]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[24],"%")))
textplain(mid = c(0.93, 0.5),
lab = c("Step3: Sulfur",
"oxidation",
paste("Genomes:",input.total$Nb.Genome[25]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[25],"%")))
textplain(mid = c(0.75, 0.12),
lab = c("Step4: Sulfite oxidation",
paste("Genomes:",input.total$Nb.Genome[26]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[26],"%")))
textplain(mid = c(0.25, 0.20),
lab = c("Step5: Sulfate reduction",
paste("Genomes:",input.total$Nb.Genome[27]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[27],"%")))
textplain(mid = c(0.23, 0.75),
lab = c("Step6: Sulfite reduction",
paste("Genomes:",input.total$Nb.Genome[28]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[28],"%")))
textplain(mid = c(0.41, 0.35),
lab = c("Step7: Thiosulfate oxidation",
paste("Genomes:",input.total$Nb.Genome[29]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[29],"%")))
textplain(mid = c(0.45, 0.62),
lab = c("Step8: Thiosulfate disproportionation 1",
paste("Genomes:",input.total$Nb.Genome[30]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[30],"%")))
textplain(mid = c(0.68, 0.40),
lab = c("Step9: Thiosulfate disproportionation 2",
paste("Genomes:",input.total$Nb.Genome[31]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[31],"%")))
input <- read.table("~/Desktop/Sulfitobacter_sp_UWMA-0305.R_input.txt", sep="\t")
View(input)
openplotmat()
#par(mar = c(2, 2, 2, 2))
openplotmat(main = "Nitrogen Cycle: Summary Figure") # Add a tiitl
elpos <- coordinates (c(1, 2, 2, 2, 1)) # Put the coordinat
straightarrow(from = elpos[1, ], to = elpos[3, ], lty = 1, lcol = 1) #N-S-01:Nitrogen fixation
straightarrow(from = elpos[3, ], to = elpos[7, ], lty = 1, lcol = 1) #N-S-02:Ammonia oxidation
straightarrow(from = elpos[7, ], to = elpos[8, ], lty = 1, lcol = 1) #N-S-03:Nitrite oxidation
straightarrow(from = elpos[8, ], to = elpos[6, ], lty = 1, lcol = 1) #N-S-04:Nitrate reduction
straightarrow(from = elpos[6, ], to = elpos[4, ], lty = 1, lcol = 1) #N-S-05:Nitrite reduction
straightarrow(from = elpos[4, ], to = elpos[2, ], lty = 1, lcol = 1) #N-S-06:Nitric oxide reduction
straightarrow(from = elpos[2, ], to = elpos[1, ], lty = 1, lcol = 1) #N-S-07:Nitrous oxide reduction
splitarrow(from = elpos[c(3,6), ], to = elpos[1, ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = 1) #N-S-08:Nitrite ammonification
straightarrow(from = elpos[8, ], to = elpos[3, ], lty = 1, lcol = 1) #N-S-09:Anammox
textrect (elpos[1, ], 0.05, 0.05, lab = expression(paste(N['2'],' ',(0))), cex = 1.5)
textrect (elpos[2, ], 0.07, 0.05, lab = expression(paste(N['2'],O,' ',(+1))), cex = 1.5)
textrect (elpos[3, ], 0.07, 0.05, lab = expression(paste(NH['4'])^'+'* ' '(-3)), cex = 1.5)
textrect (elpos[4, ], 0.07, 0.05, lab = expression(paste(NO,' ',(+2))), cex = 1.5)
textrect (elpos[6, ], 0.07, 0.05, lab = expression(paste(NO['2'])^'-'* ' '(+3)), cex = 1.5)
textrect (elpos[7, ], 0.07, 0.05, lab = expression(paste(NO['2'])^'-'* ' '(+3)), cex = 1.5)
textrect (elpos[8, ], 0.07, 0.05, lab = expression(paste(NO['3'])^'-'* ' '(+5)), cex = 1.5)
# To know where to write the names (mid = c(X,Y), I ploted elpost (plot(elpos) to get approximate coordinates))
# Make spacing between lines smaller:
par(lheight=0.05)
textplain(mid = c(0.7, 0.85),
lab = c("Step1: Nitrogen fixation",
paste("Genomes:",input.total$Nb.Genome[10]),
paste("Coverage:",input.total$Genome.Coverage.Percentages.Round[10],"%")))
openplotmat()
par(mar = c(2, 2, 2, 2))
openplotmat(main = paste("Sulfur Cycle:", name.of.genome)) # Add a title
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
elpos
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = input[23,2]) #S-S-01:Sulfide oxidation
straightarrow(from = elpos[4, ], to = elpos[1, ], lty = 1, lcol = input[24,2]) #S-S-02:Sulfur reduction
openplotmat()
par(mar = c(2, 2, 2, 2))
openplotmat(main = paste("Sulfur Cycle:", name.of.genome)) # Add a title
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
elpos
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = input[23,2]) #S-S-01:Sulfide oxidation
input$V2 <- input$V2+1
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = input[23,2]) #S-S-01:Sulfide oxidation
straightarrow(from = elpos[4, ], to = elpos[1, ], lty = 1, lcol = input[24,2]) #S-S-02:Sulfur reduction
straightarrow(from = elpos[4, ], to = elpos[10, ], lty = 1, lcol = input[25,2]) #S-S-03:Sulfur oxidation
straightarrow(from = elpos[10, ], to = elpos[11, ], lty = 1, lcol = input[26,2]) #S-S-04:Sulfite oxidation
straightarrow(from = elpos[11, ], to = elpos[5, ], lty = 1, lcol = input[27,2]) #S-S-05:Sulfate reduction
straightarrow(from = elpos[5, ], to = elpos[1, ], lty = 1, lcol = input[28,2]) #S-S-06:Sulfite reduction
straightarrow(from = elpos[6, ], to = elpos[11, ], lty = 1, lcol = input[29,2]) #S-S-07:Thiosulfate oxidation
splitarrow(from = elpos[6, ], to = elpos[c(1,10), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = input[30,2]) #S-S-08:Thiosulfate disproportionation
splitarrow(from = elpos[6, ], to = elpos[c(4,11), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = input[31,2]) #S-S-09:Thiosulfate disproportionation 2
textrect (elpos[1, ], 0.07, 0.05, lab = expression(paste(H['2'],S,' ',(-2))), cex = 1.5)
textrect (elpos[4, ], 0.05, 0.05, lab = expression(paste(S,' ',(0))), cex = 1.5)
textrect (elpos[5, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[6, ], 0.07, 0.05, lab = expression(paste(S['2']*O['3'])^'2-'* ' '(+2)), cex = 1.5)
textrect (elpos[10, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[11, ], 0.07, 0.05, lab = expression(paste(SO['4'])^'2-'*' '(+6)), cex = 1.5)
par(lheight=0.08)
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation"))
textplain(mid = c(0.68, 0.69),
lab = c("Step2: Sulfur reduction"))
textplain(mid = c(0.93, 0.5),
lab = c("Step3: Sulfur oxidation"))
textplain(mid = c(0.75, 0.15),
lab = c("Step4: Sulfite oxidation"))
textplain(mid = c(0.25, 0.23),
lab = c("Step5: Sulfate reduction"))
textplain(mid = c(0.23, 0.75),
lab = c("Step6: Sulfite reduction"))
textplain(mid = c(0.605, 0.32),
lab = c("Step7: Thiosulfate oxidation"))
textplain(mid = c(0.45, 0.61),
lab = c("Step8: Thiosulfate disproportionation 1"))
textplain(mid = c(0.68, 0.40),
lab = c("Step8: Thiosulfate disproportionation 2"))
textplain(mid = c(0.68, 0.40),
lab = c("Step9: Thiosulfate disproportionation 2"))
openplotmat()
par(mar = c(2, 2, 2, 2))
openplotmat(main = paste("Sulfur Cycle:", name.of.genome)) # Add a title
elpos <- coordinates (c(1, 3, 3, 3, 1)) # Put the coordinate
elpos
straightarrow(from = elpos[1, ], to = elpos[4, ], lty = 1, lcol = input[23,2]) #S-S-01:Sulfide oxidation
straightarrow(from = elpos[4, ], to = elpos[1, ], lty = 1, lcol = input[24,2]) #S-S-02:Sulfur reduction
straightarrow(from = elpos[4, ], to = elpos[10, ], lty = 1, lcol = input[25,2]) #S-S-03:Sulfur oxidation
straightarrow(from = elpos[10, ], to = elpos[11, ], lty = 1, lcol = input[26,2]) #S-S-04:Sulfite oxidation
straightarrow(from = elpos[11, ], to = elpos[5, ], lty = 1, lcol = input[27,2]) #S-S-05:Sulfate reduction
straightarrow(from = elpos[5, ], to = elpos[1, ], lty = 1, lcol = input[28,2]) #S-S-06:Sulfite reduction
straightarrow(from = elpos[6, ], to = elpos[11, ], lty = 1, lcol = input[29,2]) #S-S-07:Thiosulfate oxidation
splitarrow(from = elpos[6, ], to = elpos[c(1,10), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = input[30,2]) #S-S-08:Thiosulfate disproportionation
splitarrow(from = elpos[6, ], to = elpos[c(4,11), ], lty = 1, lwd = 1, dd = 0.7, arr.side = 1:2, lcol = input[31,2]) #S-S-09:Thiosulfate disproportionation 2
textrect (elpos[1, ], 0.07, 0.05, lab = expression(paste(H['2'],S,' ',(-2))), cex = 1.5)
textrect (elpos[4, ], 0.05, 0.05, lab = expression(paste(S,' ',(0))), cex = 1.5)
textrect (elpos[5, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[6, ], 0.07, 0.05, lab = expression(paste(S['2']*O['3'])^'2-'* ' '(+2)), cex = 1.5)
textrect (elpos[10, ], 0.07, 0.05, lab = expression(paste(SO['3'])^'2-'*' '(+4)), cex = 1.5)
textrect (elpos[11, ], 0.07, 0.05, lab = expression(paste(SO['4'])^'2-'*' '(+6)), cex = 1.5)
par(lheight=0.08)
textplain(mid = c(0.8, 0.85),
lab = c("Step1: Sulfide oxidation"))
textplain(mid = c(0.68, 0.69),
lab = c("Step2: Sulfur reduction"))
textplain(mid = c(0.93, 0.5),
lab = c("Step3: Sulfur oxidation"))
textplain(mid = c(0.75, 0.15),
lab = c("Step4: Sulfite oxidation"))
textplain(mid = c(0.25, 0.23),
lab = c("Step5: Sulfate reduction"))
textplain(mid = c(0.23, 0.75),
lab = c("Step6: Sulfite reduction"))
textplain(mid = c(0.605, 0.32),
lab = c("Step7: Thiosulfate oxidation"))
textplain(mid = c(0.45, 0.61),
lab = c("Step8: Thiosulfate disproportionation 1"))
textplain(mid = c(0.68, 0.40),
lab = c("Step9: Thiosulfate disproportionation 2"))
paste(R_input_table,"Metabolic_energy_flow_input.txt")
R_input_table<-"/path/"
paste(R_input_table,"Metabolic_energy_flow_input.txt")
paste(R_input_table,"Metabolic_energy_flow_input.txt",sep="")
library("tidygraph", lib.loc="/Library/Frameworks/R.framework/Versions/3.5/Resources/library")
library("igraph", lib.loc="/Library/Frameworks/R.framework/Versions/3.5/Resources/library")
library("ggraph", lib.loc="/Library/Frameworks/R.framework/Versions/3.5/Resources/library")
#R_input_table <- "/Users/patriciatran/Downloads/Metabolic_network_input.txt"
table <- read.csv(R_input_table, header=T, sep="\t")
R_input_table <- "/Users/patriciatran/Downloads/Metabolic_network_input.txt"
table <- read.csv(R_input_table, header=T, sep="\t")
View(table)
#install.packages("ggraph")
library(ggraph)
library(igraph)
library(tidyverse)
library(tidygraph)
my_graph <- table[,c(2,3,4,5)] %>%
graph_from_data_frame()
deg <- degree(my_graph, mode="all")
View(table)
View(my_graph)
View(table)
# this generates the whole community plot
community.plot <- table[,c(2,3,4,5)] %>%
graph_from_data_frame() %>%
ggraph(layout = "linear",circular = TRUE) +
geom_edge_arc(alpha = .25,
aes(width = Coverage.value.average., color=as.factor(Taxonomic.Group))) +
geom_node_point(color = "black", size = 0.02*deg, alpha=0.75) +
geom_node_text(aes(label = name), color="black", repel = TRUE)+
#theme_graph()+
labs(title = 'Metabolic connections within dataset',
subtitle = 'No scaling')
plot.name <- paste0(network.plots.folder,"/CommunityPlot.PDF")
print(plot.name)
# this generates the whole community plot
community.plot <- table[,c(2,3,4,5)] %>%
graph_from_data_frame() %>%
ggraph(layout = "linear",circular = TRUE) +
geom_edge_arc(alpha = .25,
aes(width = Coverage.value.average., color=as.factor(Taxonomic.Group))) +
geom_node_point(color = "black", size = 0.02*deg, alpha=0.75) +
geom_node_text(aes(label = name), color="black", repel = TRUE)+
#theme_graph()+
labs(title = 'Metabolic connections within dataset',
subtitle = 'No scaling')
community.plot
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(lubridate)
library(RColorBrewer)
#Cys Individual plots of all sources
ggplot(Cys, aes(source)) +
geom_bar(aes(fill = query_name))
Cys <- read.csv("~/Downloads/Cys_Combined_Individual.csv")
ggplot(Cys, aes(source)) +
geom_bar(aes(fill = query_name))
Cys <- read.csv("~/Downloads/Cys_Combined_Individual.csv")
ggplot(Cys, aes(source)) +
geom_bar(aes(fill = query_name))
ggplot(Cys, aes(source)) +
geom_bar() +
facet_wrap(~query_name)
Cys %>%
filter(Evalue >= 1e-50) %>%
ggplot(aes(source)) +
geom_bar(aes(fill = query_name))
#Cys LM only
Cys_LM <- Cys %>%
filter(source == "LM_Time")
#Adding GaID column
Cys_LM$GaID <- Cys_LM$target_name
Cys_LM$GaID <- str_replace(Cys_LM$GaID, "_.*", "")
R_input_table <- "/Users/patriciatran/Downloads/Metabolic_network_input.txt"
table <- read.csv(R_input_table, header=T, sep="\t")
View(table)