text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)#
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)#
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)#
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)#
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)#
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
library("maps")
library("mapdata")
library("mapproj")
map("state", "washington", fill=T, col="palegreen3", boundary=F)
x<-c(-122.753796, -122.827754, -122.852089, -123.052859, -122.361794, -122.65349, -122.63235, -122.38929)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
x1<-c(-122.753796, -122.827754, -122.361794, -122.65349, -122.63235, -122.38929)#
y1<-c(48.976076, 47.597041, 47.599821, 47.542182, 47.138708, 47.276488)
points(x1,y1, pch=21, bg="red")
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)#
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)#
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)#
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)#
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)#
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
?merge
library(affy)
?edge
library(edgeR)
?edgeR
edgeR
edge
?edge
?seacarb
?pgas
library(seacarb)
?seacarb
?pgas
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")#
development<-read.csv("OADev1.csv", sep=",", header=T)#
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
error.bar<-function(x,y,upper, lower=upper, length=0.1)#
{if(length(x) !=length(y)|length(y) !=length(lower)|length(lower) !=length(upper))#
	stop("vectors must be same length")#
	arrows(x,y+upper, x, y-lower, angle=90, code=3, length=length)#
	}
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
T1380<-development$Percent[1]
development<-read.csv("OADev1.csv", sep=",", header=T)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
getwd()
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
getwd()
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
development<-read.csv("OADev1.csv", sep=",", header=T)
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
error.bar<-function(x,y,upper, lower=upper, length=0.1)#
{if(length(x) !=length(y)|length(y) !=length(lower)|length(lower) !=length(upper))#
	stop("vectors must be same length")#
	arrows(x,y+upper, x, y-lower, angle=90, code=3, length=length)#
	}
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
T1380
T1840
T2380
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.15, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.1, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.05, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.6))
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
y.err.cleav<-c(sd(raw.dev$development[1:3]),sd(raw.dev$development[4:6]),sd(raw.dev$development[7:9]),sd(raw.dev$development[10:12]) )
error.bar(bar.clv,plot.cleav,y.err.cleav)
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.6))
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.62))
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.65))
error.bar(bar.clv,cleav.mat,y.err.cleav)
hatch.dat<-c(T3380, T3840, T4380,T4840, T5380,T5840)
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0.1,0.5), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
T3380
T3840
T4380
T4840
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0,0,1,0,1,0,1), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0,0,1,0,1,0), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
y.err.hatch<-c(sd(raw.dev$development[13:15]),sd(raw.dev$development[6:18]),sd(raw.dev$development[19:21]),sd(raw.dev$development[22:24]),sd(raw.dev$development[25:27]),sd(raw.dev$development[28:30]))
error.bar(bar.hatch,hatch.dat,y.err.hatch)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
development<-read.csv("OADev1.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.65))
?setwd
library(seacarb)
c(1,2,3,4,5)
1:5
help(package='seacarb')
?seacarb
amp(s=35,T=25)
amp(S=35,T=25)
?alkalinity
alkalinity
data(alkalinity)
p2fCO2(T=16, 860)
p2fCO2(T=16, pCO2=860)
library(seacarb)
p2fCO2
f2pCO2
bjerrum
library(seacarb)
p2fCO2
f2pCO2
amp
buffer
carb
library(seacarb)
p2fCO2(T=25, pCO2=380)
p2fCO2
alkalinit
alkalinity
bjerrum
amp
p2fco2
p2fCO2
?aov
?TukeyHSD
?aov
?model.aov
?model
?ordi.monte
source("/Users/emmatimminsschiffman/Documents/Autumn 2010/Multivariate Stats/biostats.R")
ordi.monte
olyblast<-c(41136, 21748, 11101, 6015, 2089, 1672, 793)
barplot(olyblast)
color.blast<-c('darkviolet', 'thistle4', 'slategray1', 'seagreen4', 'sienna4', 'mistyrose', 'ghostwhite')
barplot(olyblast, col=color.blast)
barplot(olyblast, col=color.blast, names=c('O. lurida', 'C. gigas', 'P. fuctata', 'D. rerio', 'H. midae', 'R. philippinarum', 'H. kamtschatkana'), las=2)
barplot(olyblast, col=color.blast, names=c('O. lurida', 'C. gigas', 'P. fuctata', 'D. rerio', 'H. midae', 'R. philippinarum', 'H. kamtschatkana'), las=2, cex.names=0.75)
barplot(olyblast, col=color.blast, names=c('O. lurida', 'C. gigas', 'P. fuctata', 'D. rerio', 'H. midae', 'R. philippinarum', 'H. kamtschatkana'), las=2, cex.names=0.5)
barplot(olyblast, col=color.blast, names=c('O. lurida', 'C. gigas', 'P. fuctata', 'D. rerio', 'H. midae', 'R. philippinarum', 'H. kamtschatkana'), las=2, cex.names=0.6)
barplot(olyblast, col=color.blast, names=c('O. lurida', 'C. gigas', 'P. fuctata', 'D. rerio', 'H. midae', 'R. philippinarum', 'H. kamtschatkana'), las=2, cex.names=0.6, cex.lab=0.6)
barplot(olyblast, col=color.blast, names=c('O. lurida', 'C. gigas', 'P. fuctata', 'D. rerio', 'H. midae', 'R. philippinarum', 'H. kamtschatkana'), las=2, cex.names=0.6, cex.axis=0.6)
pintoblast<-c(8641, 3090, 909, 798, 670, 596, 515)
color.blast2<-c('ghostwhite', 'sienna4', 'thistle4', 'darkviolet', 'seagreen4', 'slategray1', 'mistyrose')
barplot(pintoblast, col=color.blast2, names=c('H. kamtschatkana', 'H. midae', 'C. gigas', 'O. lurida', 'D. rerio', 'P. fuctata', 'R. philippinarum'), las=2, cex.names=0.6, cex.axis=0.6)
install.packages('ggplot2')
library(ggplot2)
revigo.names <- c("term_ID","description","frequency_%","plot_X","plot_Y","plot_size","log10_p_value","uniqueness","dispensability");
revigo.data <- rbind(c("GO:0006897","endocytosis", 0.075, 1.898, 3.313, 3.934,-2.7810,0.957,0.000),
c("GO:0007156","homophilic cell adhesion", 0.071,-0.751,-0.783, 3.910,-19.6271,0.930,0.000),
#
c("GO:0022610","biological adhesion", 0.544,-0.301, 1.227, 4.792,-11.4584,0.983,0.000),
#
c("GO:0048589","developmental growth", 0.053, 4.714, 4.079, 3.782,-1.0079,0.736,0.000),
#
c("GO:0010324","membrane invagination", 0.005, 4.829,-1.873, 2.777,-2.7810,0.864,0.014),
#
c("GO:0008037","cell recognition", 0.025, 6.272, 3.805, 3.458,-3.6737,0.708,0.016),
#
c("GO:0007218","neuropeptide signaling pathway", 0.049,-5.379, 2.516, 3.747,-3.8570,0.786,0.017),
#
c("GO:0009190","cyclic nucleotide biosynthetic process", 0.444, 0.530,-2.714, 4.704,-3.3279,0.875,0.019),
#
c("GO:0008218","bioluminescence", 0.013,-0.119, 3.383, 3.169,-2.5467,0.964,0.034),
#
c("GO:0051604","protein maturation", 0.132,-1.294,-6.233, 4.177,-2.9188,0.926,0.051),
#
c("GO:0070085","glycosylation", 0.177, 1.062,-4.331, 4.304,-1.3647,0.955,0.052),
#
c("GO:0009100","glycoprotein metabolic process", 0.119, 2.857,-5.345, 4.134,-1.0160,0.940,0.101),
#
c("GO:0051043","regulation of membrane protein ectodomain proteolysis", 0.003,-4.197,-4.405, 2.468,-1.6282,0.840,0.192),
#
c("GO:0015711","organic anion transport", 0.168, 1.816, 0.856, 4.281,-1.0502,0.971,0.202),
#
c("GO:0010817","regulation of hormone levels", 0.046,-5.470,-0.989, 3.718,-1.9001,0.865,0.210),
#
c("GO:0018209","peptidyl-serine modification", 0.013,-0.556,-7.025, 3.177,-1.6050,0.906,0.212),
#
c("GO:0034311","diol metabolic process", 0.059, 1.595,-2.192, 3.824,-1.0243,0.938,0.217),
#
c("GO:0045471","response to ethanol", 0.008,-3.549, 5.096, 2.959,-1.5696,0.880,0.232),
#
c("GO:0007631","feeding behavior", 0.010,-4.270, 6.235, 3.076,-1.3486,0.885,0.235),
#
c("GO:0009612","response to mechanical stimulus", 0.014,-3.366, 6.043, 3.205,-2.1668,0.856,0.240),
#
c("GO:0016485","protein processing", 0.123,-2.575,-5.869, 4.146,-2.6296,0.909,0.248),
#
c("GO:0050778","positive regulation of immune response", 0.035,-5.498, 3.247, 3.603,-1.7783,0.698,0.254),
#
c("GO:0001919","regulation of receptor recycling", 0.001,-6.903,-0.499, 2.210,-1.3542,0.858,0.291),
#
c("GO:0006952","defense response", 0.920,-4.793, 4.809, 5.021,-1.8536,0.842,0.321),
#
c("GO:0007259","JAK-STAT cascade", 0.010,-5.963, 2.435, 3.063,-2.3612,0.812,0.326),
#
c("GO:0018149","peptide cross-linking", 0.009,-0.194,-7.077, 3.019,-1.1996,0.908,0.339),
#
c("GO:0006508","proteolysis", 4.526,-1.903,-6.151, 5.712,-2.4539,0.911,0.339),
#
c("GO:0000209","protein polyubiquitination", 0.010,-0.298,-6.611, 3.075,-1.2059,0.907,0.341),
#
c("GO:0009628","response to abiotic stimulus", 0.404,-4.728, 5.570, 4.664,-1.0527,0.859,0.388),
#
c("GO:0006486","protein glycosylation", 0.109,-0.562,-5.939, 4.093,-1.3647,0.877,0.392),
#
c("GO:0030030","cell projection organization", 0.278, 4.520,-1.491, 4.500,-1.9297,0.822,0.404),
#
c("GO:0007166","cell surface receptor signaling pathway", 1.240,-5.286, 2.727, 5.150,-1.3373,0.753,0.457),
#
c("GO:0018298","protein-chromophore linkage", 0.160,-1.145,-6.683, 4.260,-1.1420,0.894,0.466),
#
c("GO:0060249","anatomical structure homeostasis", 0.024,-5.695,-0.757, 3.428,-1.6780,0.870,0.483),
#
c("GO:0001890","placenta development", 0.014, 5.579, 3.321, 3.206,-2.7156,0.625,0.485),
#
c("GO:0042445","hormone metabolic process", 0.025,-5.234,-0.774, 3.460,-2.0264,0.848,0.486),
#
c("GO:0042060","wound healing", 0.047,-5.309, 4.905, 3.732,-1.4511,0.853,0.492),
#
c("GO:0042733","embryonic digit morphogenesis", 0.005, 5.585, 3.609, 2.768,-1.0465,0.655,0.499),
#
c("GO:0007368","determination of left/right symmetry", 0.010, 6.178, 3.474, 3.057,-1.7100,0.640,0.517),
#
c("GO:0009611","response to wounding", 0.115,-4.868, 5.123, 4.117,-1.3453,0.860,0.530),
#
c("GO:0050982","detection of mechanical stimulus", 0.004,-3.101, 6.425, 2.610,-2.2029,0.863,0.574),
#
c("GO:0007600","sensory perception", 0.411, 6.410, 3.034, 4.671,-3.4815,0.650,0.604),
#
c("GO:0006910","phagocytosis, recognition", 0.001, 5.364, 2.528, 2.137,-1.6960,0.715,0.609),
#
c("GO:0006959","humoral immune response", 0.017,-4.162, 5.114, 3.297,-1.2507,0.797,0.622),
#
c("GO:0016044","cellular membrane organization", 0.166, 5.145,-1.959, 4.276,-1.2933,0.838,0.623),
#
c("GO:0007409","axonogenesis", 0.041, 5.862, 1.841, 3.672,-2.7519,0.518,0.626),
#
c("GO:0042176","regulation of protein catabolic process", 0.024,-4.311,-3.971, 3.442,-1.2748,0.835,0.638),
#
c("GO:0060541","respiratory system development", 0.025, 6.034, 3.026, 3.455,-1.3250,0.618,0.644),
#
c("GO:0007389","pattern specification process", 0.066, 6.230, 3.304, 3.875,-1.1858,0.615,0.649),
#
c("GO:0002541","activation of plasma proteins involved in acute inflammatory response", 0.000,-6.011,-1.077, 1.519,-1.6282,0.832,0.680),
#
c("GO:0007507","heart development", 0.047, 6.142, 2.934, 3.729,-2.0732,0.601,0.685),
#
c("GO:0030879","mammary gland development", 0.018, 5.787, 3.228, 3.302,-1.4278,0.617,0.694))
one.data <- data.frame(revigo.data);
names(one.data) <- revigo.names;
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );
one.data$frequency <- as.numeric( as.character(one.data$frequency) );
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) );
p1 <- ggplot( data = one.data );
#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();
#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );
#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();
#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );
#
ex <- one.data [ one.data$dispensability < 0.15, ]; 
#
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );
#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");
#
p1 <- p1 + opts(legend.key = theme_blank()) ;
#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);
#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);
#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);
#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10)
p1;
revigo.names <- c("term_ID","description","frequency_%","plot_X","plot_Y","plot_size","log10_p_value","uniqueness","dispensability");
#
revigo.data <- rbind(c("GO:0006410","transcription, RNA-dependent", 0.154,-5.983, 1.086, 4.210,-2.7374,0.735,0.000),
#
c("GO:0009651","response to salt stress", 0.037, 6.331,-0.686, 3.621,-1.2520,0.735,0.000),
#
c("GO:0015979","photosynthesis", 0.922, 2.485,-5.575, 5.021,-1.9802,0.731,0.000),
#
c("GO:0016032","viral reproduction", 2.702,-3.671,-4.689, 5.488,-2.3115,0.741,0.000),
#
c("GO:0019079","viral genome replication", 0.538, 4.020, 5.089, 4.787,-2.7374,0.394,0.000),
#
c("GO:0042254","ribosome biogenesis", 0.842,-2.137, 5.974, 4.982,-1.3645,0.730,0.026));
one.data <- data.frame(revigo.data);
#
names(one.data) <- revigo.names;
#
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];
#
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );
#
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );
#
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );
#
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );
#
one.data$frequency <- as.numeric( as.character(one.data$frequency) );
#
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );
#
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) );
p1 <- ggplot( data = one.data );
#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();
#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );
#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();
#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );
#
ex <- one.data [ one.data$dispensability < 0.15, ]; 
#
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );
#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");
#
p1 <- p1 + opts(legend.key = theme_blank()) ;
#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);
#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);
#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);
#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10);
p1;
olyblast<-c(52.8, 27, 14.6, 5.1, 4.1, 1.9)
color.blast<-c('thistle4', 'slategray1', 'seagreen4', 'sienna4', 'mistyrose', 'ghostwhite')
barplot(olyblast, col=color.blast, names=c('C. gigas', 'P. fuctata', 'D. rerio', 'H. midae', 'R. philippinarum', 'H. kamtschatkana'), las=2, cex.names=0.6, cex.axis=0.85, ylab='Percent Coverage of O. lurida Transcriptome')
barplot(olyblast, col=color.blast, names=c('C. gigas', 'P. fuctata', 'D. rerio', 'H. midae', 'R. philippinarum', 'H. kamtschatkana'), las=2, cex.names=0.6, cex.axis=0.85, ylab='Percent Coverage of O. lurida Transcriptome', ylim=c(0,100))
pintoblast<-c(35.8, 10.5, 9.2, 7.8, 6.9, 6)
color.blast2<-c('sienna4', 'thistle4', 'darkviolet', 'seagreen4', 'slategray1', 'mistyrose')
barplot(pintoblast, col=color.blast2, names=c('H. midae', 'C. gigas', 'O. lurida', 'D. rerio', 'P. fuctata', 'R. philippinarum'), las=2, cex.names=0.6, cex.axis=0.85, ylab='Percent Coverage of H. kamtschatkana Transcriptome', ylim=c(0,100))
revigo.names <- c("term_ID","description","frequency_%","plot_X","plot_Y","plot_size","log10_p_value","uniqueness","dispensability");
#
revigo.data <- rbind(c("GO:0006800","oxygen and reactive oxygen species metabolic process", 0.154, 1.858, 0.396, 4.210,-2.0916,0.993,0.000),
#
c("GO:0007626","locomotory behavior", 0.020,-1.112, 1.133, 3.364,-1.6635,0.971,0.000),
#
c("GO:0008283","cell proliferation", 0.143, 0.694,-0.161, 4.213,-1.0233,0.993,0.000),
#
c("GO:0008380","RNA splicing", 0.170,-4.408,-0.013, 4.287,-10.7570,0.873,0.000),
#
c("GO:0016192","vesicle-mediated transport", 0.348, 0.764, 3.164, 4.598,-3.0506,0.963,0.000),
#
c("GO:0022610","biological adhesion", 0.544, 1.207, 0.368, 4.792,-2.2067,0.993,0.000),
#
c("GO:0055114","oxidation-reduction process",16.676, 1.629, 0.426, 6.279,-6.6635,0.982,0.013),
#
c("GO:0030716","oocyte fate determination", 0.001, 6.988,-3.504, 1.949,-2.6073,0.831,0.014),
#
c("GO:0035088","establishment or maintenance of apical/basal cell polarity", 0.002, 0.328, 0.023, 2.453,-1.3493,0.967,0.015),
#
c("GO:0007163","establishment or maintenance of cell polarity", 0.016, 1.499, 0.542, 3.262,-1.3900,0.971,0.016),
#
c("GO:0030029","actin filament-based process", 0.106, 0.178,-0.029, 4.084,-6.2848,0.968,0.019),
#
c("GO:0007010","cytoskeleton organization", 0.203, 4.735, 6.336, 4.363,-10.4486,0.734,0.020),
#
c("GO:0007017","microtubule-based process", 0.308, 0.566, 0.210, 4.546,-5.2226,0.965,0.021),
#
c("GO:0000910","cytokinesis", 0.236, 1.601, 0.587, 4.429,-1.2966,0.966,0.021),
#
c("GO:0045454","cell redox homeostasis", 0.541,-2.252, 6.619, 4.790,-4.6421,0.830,0.022),
#
c("GO:0007155","cell adhesion", 0.540, 0.897,-0.558, 4.789,-2.3218,0.949,0.024),
#
c("GO:0042743","hydrogen peroxide metabolic process", 0.046, 0.049,-0.207, 3.718,-1.8137,0.950,0.035),
#
c("GO:0017144","drug metabolic process", 0.079, 1.661, 0.611, 3.954,-1.4425,0.953,0.036),
#
c("GO:0015980","energy derivation by oxidation of organic compounds", 4.971, 0.029,-1.557, 5.753,-9.0182,0.887,0.052),
#
c("GO:0006518","peptide metabolic process", 0.211, 0.787,-0.160, 4.381,-1.4665,0.950,0.054),
#
c("GO:0006084","acetyl-CoA metabolic process", 0.531,-0.875,-1.660, 4.782,-6.2684,0.897,0.060),
#
c("GO:0006006","glucose metabolic process", 1.107,-2.536,-4.315, 5.101,-8.4908,0.805,0.065),
#
c("GO:0009820","alkaloid metabolic process", 0.004, 0.980,-0.151, 2.614,-2.7758,0.962,0.077),
#
c("GO:0051186","cofactor metabolic process", 3.543, 0.040, 0.069, 5.606,-3.3125,0.937,0.077),
#
c("GO:0006091","generation of precursor metabolites and energy", 6.142, 0.623,-0.201, 5.845,-18.0615,0.934,0.085),
#
c("GO:0043603","cellular amide metabolic process", 0.201,-0.518,-1.157, 4.361,-1.3966,0.926,0.108),
#
c("GO:0006890","retrograde vesicle-mediated transport, Golgi to ER", 0.005, 1.319, 3.630, 2.757,-1.6644,0.933,0.176),
#
c("GO:0048678","response to axon injury", 0.005,-1.154, 0.732, 2.717,-1.0101,0.968,0.214),
#
c("GO:0006090","pyruvate metabolic process", 0.041,-2.007,-3.845, 3.667,-4.3215,0.891,0.227),
#
c("GO:0006414","translational elongation", 0.665,-5.221, 0.298, 4.880,-6.7905,0.856,0.251),
#
c("GO:0051443","positive regulation of ubiquitin-protein ligase activity", 0.002,-4.697, 4.427, 2.332,-3.1308,0.797,0.259),
#
c("GO:0008104","protein localization", 1.847, 0.620, 3.155, 5.323,-2.8214,0.936,0.277),
#
c("GO:0001539","ciliary or flagellar motility", 0.387, 0.225, 2.329, 4.645,-2.3615,0.932,0.280),
#
c("GO:0010608","posttranscriptional regulation of gene expression", 0.218,-4.398, 5.559, 4.395,-2.4001,0.860,0.289),
#
c("GO:0006458","'de novo' protein folding", 0.014,-3.541,-0.418, 3.201,-1.7523,0.904,0.296),
#
c("GO:0015985","energy coupled proton transport, down electrochemical gradient", 0.663, 0.574, 2.899, 4.879,-2.4501,0.923,0.297),
#
c("GO:0016071","mRNA metabolic process", 0.719,-6.026,-1.368, 4.913,-7.6253,0.876,0.300),
#
c("GO:0018149","peptide cross-linking", 0.009,-4.101,-0.343, 3.019,-2.2912,0.901,0.306),
#
c("GO:0006818","hydrogen transport", 1.025, 0.901, 3.433, 5.067,-2.3529,0.961,0.312),
#
c("GO:0021682","nerve maturation", 0.000, 6.949,-3.836, 1.398,-1.6685,0.841,0.315),
#
c("GO:0007264","small GTPase mediated signal transduction", 0.496,-2.983, 6.084, 4.753,-2.5153,0.847,0.320),
#
c("GO:0010498","proteasomal protein catabolic process", 0.042,-5.261,-1.329, 3.680,-2.8750,0.847,0.321),
#
c("GO:0006558","L-phenylalanine metabolic process", 0.058,-2.232,-4.159, 3.818,-2.1048,0.874,0.323),
#
c("GO:0006471","protein ADP-ribosylation", 0.013,-3.683,-0.341, 3.180,-1.0960,0.899,0.339),
#
c("GO:0009894","regulation of catabolic process", 0.238,-3.396, 4.831, 4.433,-1.5155,0.836,0.345),
#
c("GO:0006108","malate metabolic process", 0.111,-2.053,-3.984, 4.103,-1.3029,0.885,0.346),
#
c("GO:0010035","response to inorganic substance", 0.247,-1.386, 1.132, 4.449,-2.4658,0.950,0.350),
#
c("GO:0007164","establishment of tissue polarity", 0.004, 6.764,-3.366, 2.685,-1.3497,0.853,0.359),
#
c("GO:0009205","purine ribonucleoside triphosphate metabolic process", 4.768,-3.673,-3.935, 5.735,-4.6946,0.775,0.369),
#
c("GO:0006749","glutathione metabolic process", 0.072,-2.360,-4.572, 3.915,-1.5837,0.878,0.372),
#
c("GO:0006769","nicotinamide metabolic process", 0.000,-1.715,-3.752, 0.954,-2.4131,0.874,0.373),
#
c("GO:0006396","RNA processing", 2.591,-5.116,-0.789, 5.470,-1.4256,0.857,0.395),
#
c("GO:0007566","embryo implantation", 0.003, 6.449,-3.641, 2.507,-1.6644,0.834,0.397),
#
c("GO:0051289","protein homotetramerization", 0.007, 4.930, 6.755, 2.888,-1.7869,0.804,0.403),
#
c("GO:0019991","septate junction assembly", 0.000, 4.749, 6.216, 1.690,-1.1969,0.816,0.413),
#
c("GO:0006457","protein folding", 0.973,-4.392,-0.306, 5.045,-5.6180,0.875,0.426),
#
c("GO:0044087","regulation of cellular component biogenesis", 0.077, 2.289, 7.845, 3.943,-3.2426,0.769,0.428),
#
c("GO:0043484","regulation of RNA splicing", 0.006,-4.334, 4.564, 2.846,-1.9392,0.824,0.443),
#
c("GO:0001700","embryonic development via the syncytial blastoderm", 0.003, 6.337,-3.379, 2.504,-1.0998,0.832,0.446),
#
c("GO:0030721","spectrosome organization", 0.000, 4.817, 6.552, 0.699,-1.6685,0.826,0.450),
#
c("GO:0051129","negative regulation of cellular component organization", 0.045, 2.265, 7.425, 3.711,-1.8220,0.737,0.458),
#
c("GO:0051340","regulation of ligase activity", 0.003,-2.596, 6.152, 2.598,-2.3526,0.892,0.470),
#
c("GO:0035152","regulation of tube architecture, open tracheal system", 0.001, 6.080, 0.005, 2.196,-2.7903,0.745,0.472),
#
c("GO:0008340","determination of adult lifespan", 0.009, 6.407,-3.413, 3.035,-1.6606,0.825,0.473),
#
c("GO:0006085","acetyl-CoA biosynthetic process", 0.004,-1.213,-1.643, 2.697,-2.2385,0.910,0.474),
#
c("GO:0045478","fusome organization", 0.000, 4.829, 6.460, 1.279,-1.6685,0.815,0.484),
#
c("GO:0051591","response to cAMP", 0.005,-1.258, 0.746, 2.749,-1.7936,0.959,0.490),
#
c("GO:0006213","pyrimidine nucleoside metabolic process", 0.201,-3.187,-4.297, 4.359,-1.4180,0.828,0.495),
#
c("GO:0043433","negative regulation of sequence-specific DNA binding transcription factor activity", 0.009,-4.260, 4.614, 2.999,-1.0960,0.817,0.499),
#
c("GO:0007276","gamete generation", 0.062, 5.891,-4.046, 3.846,-1.4704,0.848,0.500),
#
c("GO:0007444","imaginal disc development", 0.009, 6.446,-3.405, 2.991,-1.7166,0.816,0.504),
#
c("GO:0016044","cellular membrane organization", 0.166, 5.067, 6.954, 4.276,-1.6677,0.785,0.505),
#
c("GO:0060047","heart contraction", 0.013, 5.819,-3.867, 3.159,-1.1929,0.879,0.508),
#
c("GO:0019953","sexual reproduction", 0.086, 3.339,-2.209, 3.990,-1.0008,0.959,0.510),
#
c("GO:0051084","'de novo' posttranslational protein folding", 0.014,-3.660,-0.386, 3.194,-1.0462,0.904,0.516),
#
c("GO:0048754","branching morphogenesis of a tube", 0.021, 6.380,-3.373, 3.372,-1.3150,0.814,0.526),
#
c("GO:0010927","cellular component assembly involved in morphogenesis", 0.019, 7.406, 2.247, 3.332,-1.1170,0.660,0.527),
#
c("GO:0006413","translational initiation", 0.337,-5.138, 0.300, 4.584,-1.7656,0.863,0.533),
#
c("GO:0001763","morphogenesis of a branching structure", 0.026, 6.478,-3.423, 3.470,-1.3294,0.820,0.537),
#
c("GO:0006412","translation", 4.967,-5.423, 0.276, 5.753,-5.2041,0.832,0.538),
#
c("GO:0045429","positive regulation of nitric oxide biosynthetic process", 0.004,-2.690, 5.902, 2.619,-1.0462,0.842,0.541),
#
c("GO:0009992","cellular water homeostasis", 0.000,-1.437, 6.111, 1.623,-1.6685,0.886,0.541),
#
c("GO:0006112","energy reserve metabolic process", 0.129,-0.107,-1.299, 4.169,-1.8918,0.915,0.543),
#
c("GO:0007016","cytoskeletal anchoring at plasma membrane", 0.002, 2.191, 7.245, 2.401,-3.1273,0.682,0.560),
#
c("GO:0042692","muscle cell differentiation", 0.034, 6.774,-3.330, 3.589,-2.5846,0.785,0.563),
#
c("GO:0016052","carbohydrate catabolic process", 1.399,-2.781,-2.512, 5.203,-5.3516,0.867,0.564),
#
c("GO:0035317","imaginal disc-derived wing hair organization", 0.001, 7.750, 1.636, 2.004,-1.9392,0.666,0.567),
#
c("GO:0051235","maintenance of location", 0.032,-1.949, 6.873, 3.556,-1.9771,0.861,0.584),
#
c("GO:0005977","glycogen metabolic process", 0.128,-2.440,-1.665, 4.164,-1.8918,0.840,0.589),
#
c("GO:0043933","macromolecular complex subunit organization", 1.085, 4.880, 6.508, 5.092,-2.5019,0.781,0.593),
#
c("GO:0042775","mitochondrial ATP synthesis coupled electron transport", 0.315,-0.424,-1.022, 4.555,-2.1471,0.906,0.598),
#
c("GO:0044042","glucan metabolic process", 0.249,-2.591,-1.536, 4.452,-1.3150,0.900,0.600),
#
c("GO:0000302","response to reactive oxygen species", 0.096,-1.618, 1.005, 4.039,-2.2784,0.942,0.602),
#
c("GO:0009791","post-embryonic development", 0.098, 6.683,-3.550, 4.048,-1.0400,0.805,0.606),
#
c("GO:0051881","regulation of mitochondrial membrane potential", 0.003,-1.699, 6.373, 2.477,-1.1929,0.875,0.610),
#
c("GO:0051187","cofactor catabolic process", 0.531,-2.027,-1.695, 4.781,-5.0487,0.857,0.615),
#
c("GO:0006397","mRNA processing", 0.620,-4.822,-0.359, 4.849,-8.9747,0.856,0.621),
#
c("GO:0007265","Ras protein signal transduction", 0.221,-2.956, 5.997, 4.402,-2.4889,0.855,0.623),
#
c("GO:0010324","membrane invagination", 0.005, 4.607, 6.144, 2.777,-1.5812,0.822,0.623),
#
c("GO:0006122","mitochondrial electron transport, ubiquinol to cytochrome c", 0.011,-0.080,-1.282, 3.105,-1.6685,0.925,0.627),
#
c("GO:0016339","calcium-dependent cell-cell adhesion", 0.001, 1.439,-0.992, 2.201,-1.0433,0.961,0.632),
#
c("GO:0030030","cell projection organization", 0.278, 4.677, 6.193, 4.500,-2.1762,0.754,0.635),
#
c("GO:0006559","L-phenylalanine catabolic process", 0.019,-3.253,-4.084, 3.331,-2.2959,0.838,0.636),
#
c("GO:0006911","phagocytosis, engulfment", 0.005, 4.011, 6.037, 2.743,-1.0521,0.800,0.646),
#
c("GO:0006979","response to oxidative stress", 0.231,-1.317, 0.827, 4.420,-2.0583,0.950,0.646),
#
c("GO:0060537","muscle tissue development", 0.036, 7.028,-3.549, 3.618,-1.5332,0.829,0.653),
#
c("GO:0050684","regulation of mRNA processing", 0.005,-4.394, 4.770, 2.748,-1.7936,0.831,0.653),
#
c("GO:0008064","regulation of actin polymerization or depolymerization", 0.026, 2.387, 7.863, 3.464,-7.1506,0.637,0.655),
#
c("GO:0016358","dendrite development", 0.014, 7.794, 1.720, 3.188,-1.3150,0.635,0.658),
#
c("GO:0006897","endocytosis", 0.075, 1.131, 3.355, 3.934,-1.4100,0.960,0.660),
#
c("GO:0002165","instar larval or pupal development", 0.010, 6.716,-3.572, 3.036,-1.3715,0.823,0.662),
#
c("GO:0032268","regulation of cellular protein metabolic process", 0.389,-5.544, 4.690, 4.647,-2.1629,0.775,0.664),
#
c("GO:0030163","protein catabolic process", 0.408,-4.836,-1.080, 4.667,-1.3202,0.857,0.670),
#
c("GO:0010033","response to organic substance", 0.355,-1.417, 1.182, 4.607,-1.1732,0.949,0.670),
#
c("GO:0034220","ion transmembrane transport", 1.198, 0.136, 2.096, 5.135,-2.0607,0.923,0.670),
#
c("GO:0006570","tyrosine metabolic process", 0.045,-2.154,-4.133, 3.706,-1.3029,0.876,0.672),
#
c("GO:0042554","superoxide anion generation", 0.002, 1.269,-1.060, 2.350,-1.0462,0.957,0.675),
#
c("GO:0006119","oxidative phosphorylation", 0.910,-0.125,-1.330, 5.016,-4.2692,0.905,0.680),
#
c("GO:0019362","pyridine nucleotide metabolic process", 0.466,-3.592,-4.539, 4.725,-3.9281,0.786,0.682),
#
c("GO:0006631","fatty acid metabolic process", 0.734,-2.148,-4.054, 4.923,-1.1916,0.860,0.684),
#
c("GO:0007052","mitotic spindle organization", 0.006, 4.749, 6.355, 2.839,-4.1726,0.739,0.688),
#
c("GO:0060711","labyrinthine layer development", 0.005, 6.754,-3.633, 2.740,-1.0462,0.819,0.689),
#
c("GO:0009109","coenzyme catabolic process", 0.518,-2.422,-2.497, 4.771,-5.2684,0.849,0.689),
#
c("GO:0030865","cortical cytoskeleton organization", 0.007, 4.950, 6.686, 2.873,-1.7936,0.757,0.691),
#
c("GO:0009208","pyrimidine ribonucleoside triphosphate metabolic process", 0.044,-2.712,-4.135, 3.698,-1.0960,0.830,0.694),
#
c("GO:0032989","cellular component morphogenesis", 0.840, 7.542, 2.233, 4.981,-1.0284,0.622,0.695),
#
c("GO:0051100","negative regulation of binding", 0.024,-2.219, 5.334, 3.430,-1.0433,0.890,0.699))
one.data <- data.frame(revigo.data);
#
names(one.data) <- revigo.names;
#
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];
#
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );
#
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );
#
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );
#
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );
#
one.data$frequency <- as.numeric( as.character(one.data$frequency) );
#
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );
#
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) )
p1 <- ggplot( data = one.data );
#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();
#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );
#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();
#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );
#
ex <- one.data [ one.data$dispensability < 0.15, ]; 
#
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );
#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");
#
p1 <- p1 + opts(legend.key = theme_blank()) ;
#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);
#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);
#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);
#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10)
?ggplot
library(ggplot2)
p1 <- ggplot( data = one.data );
#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();
#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );
#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();
#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );
#
ex <- one.data [ one.data$dispensability < 0.15, ]; 
#
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );
#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");
#
p1 <- p1 + opts(legend.key = theme_blank()) ;
#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);
#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);
#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);
#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10)
p1
revigo.names <- c("term_ID","description","frequency_%","plot_X","plot_Y","plot_size","log10_p_value","uniqueness","dispensability");#
revigo.data2<-rbind(c("GO:0030716","oocyte fate determination", 0.001, 6.988,-3.504, 1.949,-2.6073,0.831,0.014), c("GO:0007010","cytoskeleton organization", 0.203, 4.735, 6.336, 4.363,-10.4486,0.734,0.020), c("GO:0045454","cell redox homeostasis", 0.541,-2.252, 6.619, 4.790,-4.6421,0.830,0.022), c("GO:0006006","glucose metabolic process", 1.107,-2.536,-4.315, 5.101,-8.4908,0.805,0.065))
one.data <- data.frame(revigo.data2);#
names(one.data) <- revigo.names;#
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];#
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );#
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );#
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );#
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );#
one.data$frequency <- as.numeric( as.character(one.data$frequency) );#
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );#
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) );#
#
p1 <- ggplot( data = one.data );#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );#
ex <- one.data [ one.data$dispensability < 0.15, ]; #
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");#
p1 <- p1 + opts(legend.key = theme_blank()) ;#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10)
p1
revigo.data2<- rbind(c("GO:0006800","oxygen and reactive oxygen species metabolic process", 0.154, 1.858, 0.396, 4.210,-2.0916,0.993,0.000),
c("GO:0007626", 0.020,-1.112, 1.133, 3.364,-1.6635,0.971,0.000),#
c("GO:0008283","cell proliferation", 0.143, 0.694,-0.161, 4.213,-1.0233,0.993,0.000),#
c("GO:0008380","RNA splicing", 0.170,-4.408,-0.013, 4.287,-10.7570,0.873,0.000),#
c("GO:0016192","vesicle-mediated transport", 0.348, 0.764, 3.164, 4.598,-3.0506,0.963,0.000),#
c("GO:0022610","biological adhesion", 0.544, 1.207, 0.368, 4.792,-2.2067,0.993,0.000),#
c("GO:0055114","oxidation-reduction process",16.676, 1.629, 0.426, 6.279,-6.6635,0.982,0.013),#
c("GO:0030716","oocyte fate determination", 0.001, 6.988,-3.504, 1.949,-2.6073,0.831,0.014),#
c("GO:0035088", 0.002, 0.328, 0.023, 2.453,-1.3493,0.967,0.015),#
c("GO:0007163", 0.016, 1.499, 0.542, 3.262,-1.3900,0.971,0.016),#
c("GO:0030029", 0.106, 0.178,-0.029, 4.084,-6.2848,0.968,0.019),#
c("GO:0007010","cytoskeleton organization", 0.203, 4.735, 6.336, 4.363,-10.4486,0.734,0.020),#
c("GO:0007017", 0.308, 0.566, 0.210, 4.546,-5.2226,0.965,0.021),#
c("GO:0000910", 0.236, 1.601, 0.587, 4.429,-1.2966,0.966,0.021),#
c("GO:0045454", 0.541,-2.252, 6.619, 4.790,-4.6421,0.830,0.022),#
c("GO:0007155","cell adhesion", 0.540, 0.897,-0.558, 4.789,-2.3218,0.949,0.024),#
c("GO:0042743", 0.046, 0.049,-0.207, 3.718,-1.8137,0.950,0.035),#
c("GO:0017144","drug metabolic process", 0.079, 1.661, 0.611, 3.954,-1.4425,0.953,0.036),#
c("GO:0015980","energy derivation by oxidation of organic compounds", 4.971, 0.029,-1.557, 5.753,-9.0182,0.887,0.052),#
c("GO:0006518","peptide metabolic process", 0.211, 0.787,-0.160, 4.381,-1.4665,0.950,0.054),#
c("GO:0006084","acetyl-CoA metabolic process", 0.531,-0.875,-1.660, 4.782,-6.2684,0.897,0.060),#
c("GO:0006006","glucose metabolic process", 1.107,-2.536,-4.315, 5.101,-8.4908,0.805,0.065),#
c("GO:0009820","alkaloid metabolic process", 0.004, 0.980,-0.151, 2.614,-2.7758,0.962,0.077),#
c("GO:0051186","cofactor metabolic process", 3.543, 0.040, 0.069, 5.606,-3.3125,0.937,0.077),#
c("GO:0006091","generation of precursor metabolites and energy", 6.142, 0.623,-0.201, 5.845,-18.0615,0.934,0.085),#
c("GO:0043603","cellular amide metabolic process", 0.201,-0.518,-1.157, 4.361,-1.3966,0.926,0.108),#
c("GO:0006890","retrograde vesicle-mediated transport, Golgi to ER", 0.005, 1.319, 3.630, 2.757,-1.6644,0.933,0.176),#
c("GO:0048678","response to axon injury", 0.005,-1.154, 0.732, 2.717,-1.0101,0.968,0.214),#
c("GO:0006090","pyruvate metabolic process", 0.041,-2.007,-3.845, 3.667,-4.3215,0.891,0.227),#
c("GO:0006414","translational elongation", 0.665,-5.221, 0.298, 4.880,-6.7905,0.856,0.251),#
c("GO:0051443","positive regulation of ubiquitin-protein ligase activity", 0.002,-4.697, 4.427, 2.332,-3.1308,0.797,0.259),#
c("GO:0008104","protein localization", 1.847, 0.620, 3.155, 5.323,-2.8214,0.936,0.277),#
c("GO:0001539","ciliary or flagellar motility", 0.387, 0.225, 2.329, 4.645,-2.3615,0.932,0.280),#
c("GO:0010608","posttranscriptional regulation of gene expression", 0.218,-4.398, 5.559, 4.395,-2.4001,0.860,0.289),#
c("GO:0006458","'de novo' protein folding", 0.014,-3.541,-0.418, 3.201,-1.7523,0.904,0.296),#
c("GO:0015985","energy coupled proton transport, down electrochemical gradient", 0.663, 0.574, 2.899, 4.879,-2.4501,0.923,0.297),#
c("GO:0016071","mRNA metabolic process", 0.719,-6.026,-1.368, 4.913,-7.6253,0.876,0.300),#
c("GO:0018149","peptide cross-linking", 0.009,-4.101,-0.343, 3.019,-2.2912,0.901,0.306),#
c("GO:0006818","hydrogen transport", 1.025, 0.901, 3.433, 5.067,-2.3529,0.961,0.312),#
c("GO:0021682","nerve maturation", 0.000, 6.949,-3.836, 1.398,-1.6685,0.841,0.315),#
c("GO:0007264","small GTPase mediated signal transduction", 0.496,-2.983, 6.084, 4.753,-2.5153,0.847,0.320),#
c("GO:0010498","proteasomal protein catabolic process", 0.042,-5.261,-1.329, 3.680,-2.8750,0.847,0.321),#
c("GO:0006558","L-phenylalanine metabolic process", 0.058,-2.232,-4.159, 3.818,-2.1048,0.874,0.323),#
c("GO:0006471","protein ADP-ribosylation", 0.013,-3.683,-0.341, 3.180,-1.0960,0.899,0.339),#
c("GO:0009894","regulation of catabolic process", 0.238,-3.396, 4.831, 4.433,-1.5155,0.836,0.345),#
c("GO:0006108","malate metabolic process", 0.111,-2.053,-3.984, 4.103,-1.3029,0.885,0.346),#
c("GO:0010035","response to inorganic substance", 0.247,-1.386, 1.132, 4.449,-2.4658,0.950,0.350),#
c("GO:0007164","establishment of tissue polarity", 0.004, 6.764,-3.366, 2.685,-1.3497,0.853,0.359),#
c("GO:0009205","purine ribonucleoside triphosphate metabolic process", 4.768,-3.673,-3.935, 5.735,-4.6946,0.775,0.369),#
c("GO:0006749","glutathione metabolic process", 0.072,-2.360,-4.572, 3.915,-1.5837,0.878,0.372),#
c("GO:0006769","nicotinamide metabolic process", 0.000,-1.715,-3.752, 0.954,-2.4131,0.874,0.373),#
c("GO:0006396","RNA processing", 2.591,-5.116,-0.789, 5.470,-1.4256,0.857,0.395),#
c("GO:0007566","embryo implantation", 0.003, 6.449,-3.641, 2.507,-1.6644,0.834,0.397),#
c("GO:0051289","protein homotetramerization", 0.007, 4.930, 6.755, 2.888,-1.7869,0.804,0.403),#
c("GO:0019991","septate junction assembly", 0.000, 4.749, 6.216, 1.690,-1.1969,0.816,0.413),#
c("GO:0006457","protein folding", 0.973,-4.392,-0.306, 5.045,-5.6180,0.875,0.426),#
c("GO:0044087","regulation of cellular component biogenesis", 0.077, 2.289, 7.845, 3.943,-3.2426,0.769,0.428),#
c("GO:0043484","regulation of RNA splicing", 0.006,-4.334, 4.564, 2.846,-1.9392,0.824,0.443),#
c("GO:0001700","embryonic development via the syncytial blastoderm", 0.003, 6.337,-3.379, 2.504,-1.0998,0.832,0.446),#
c("GO:0030721","spectrosome organization", 0.000, 4.817, 6.552, 0.699,-1.6685,0.826,0.450),#
c("GO:0051129","negative regulation of cellular component organization", 0.045, 2.265, 7.425, 3.711,-1.8220,0.737,0.458),#
c("GO:0051340","regulation of ligase activity", 0.003,-2.596, 6.152, 2.598,-2.3526,0.892,0.470),#
c("GO:0035152","regulation of tube architecture, open tracheal system", 0.001, 6.080, 0.005, 2.196,-2.7903,0.745,0.472),#
c("GO:0008340","determination of adult lifespan", 0.009, 6.407,-3.413, 3.035,-1.6606,0.825,0.473),#
c("GO:0006085","acetyl-CoA biosynthetic process", 0.004,-1.213,-1.643, 2.697,-2.2385,0.910,0.474),#
c("GO:0045478","fusome organization", 0.000, 4.829, 6.460, 1.279,-1.6685,0.815,0.484),#
c("GO:0051591","response to cAMP", 0.005,-1.258, 0.746, 2.749,-1.7936,0.959,0.490),#
c("GO:0006213","pyrimidine nucleoside metabolic process", 0.201,-3.187,-4.297, 4.359,-1.4180,0.828,0.495),#
c("GO:0043433","negative regulation of sequence-specific DNA binding transcription factor activity", 0.009,-4.260, 4.614, 2.999,-1.0960,0.817,0.499),#
c("GO:0007276","gamete generation", 0.062, 5.891,-4.046, 3.846,-1.4704,0.848,0.500),#
c("GO:0007444","imaginal disc development", 0.009, 6.446,-3.405, 2.991,-1.7166,0.816,0.504),#
c("GO:0016044","cellular membrane organization", 0.166, 5.067, 6.954, 4.276,-1.6677,0.785,0.505),#
c("GO:0060047","heart contraction", 0.013, 5.819,-3.867, 3.159,-1.1929,0.879,0.508),#
c("GO:0019953","sexual reproduction", 0.086, 3.339,-2.209, 3.990,-1.0008,0.959,0.510),#
c("GO:0051084","'de novo' posttranslational protein folding", 0.014,-3.660,-0.386, 3.194,-1.0462,0.904,0.516),#
c("GO:0048754","branching morphogenesis of a tube", 0.021, 6.380,-3.373, 3.372,-1.3150,0.814,0.526),#
c("GO:0010927","cellular component assembly involved in morphogenesis", 0.019, 7.406, 2.247, 3.332,-1.1170,0.660,0.527),#
c("GO:0006413","translational initiation", 0.337,-5.138, 0.300, 4.584,-1.7656,0.863,0.533),#
c("GO:0001763","morphogenesis of a branching structure", 0.026, 6.478,-3.423, 3.470,-1.3294,0.820,0.537),#
c("GO:0006412","translation", 4.967,-5.423, 0.276, 5.753,-5.2041,0.832,0.538),#
c("GO:0045429","positive regulation of nitric oxide biosynthetic process", 0.004,-2.690, 5.902, 2.619,-1.0462,0.842,0.541),#
c("GO:0009992","cellular water homeostasis", 0.000,-1.437, 6.111, 1.623,-1.6685,0.886,0.541),#
c("GO:0006112","energy reserve metabolic process", 0.129,-0.107,-1.299, 4.169,-1.8918,0.915,0.543),#
c("GO:0007016","cytoskeletal anchoring at plasma membrane", 0.002, 2.191, 7.245, 2.401,-3.1273,0.682,0.560),#
c("GO:0042692","muscle cell differentiation", 0.034, 6.774,-3.330, 3.589,-2.5846,0.785,0.563),#
c("GO:0016052","carbohydrate catabolic process", 1.399,-2.781,-2.512, 5.203,-5.3516,0.867,0.564),#
c("GO:0035317","imaginal disc-derived wing hair organization", 0.001, 7.750, 1.636, 2.004,-1.9392,0.666,0.567),#
c("GO:0051235","maintenance of location", 0.032,-1.949, 6.873, 3.556,-1.9771,0.861,0.584),#
c("GO:0005977","glycogen metabolic process", 0.128,-2.440,-1.665, 4.164,-1.8918,0.840,0.589),#
c("GO:0043933","macromolecular complex subunit organization", 1.085, 4.880, 6.508, 5.092,-2.5019,0.781,0.593),#
c("GO:0042775","mitochondrial ATP synthesis coupled electron transport", 0.315,-0.424,-1.022, 4.555,-2.1471,0.906,0.598),#
c("GO:0044042","glucan metabolic process", 0.249,-2.591,-1.536, 4.452,-1.3150,0.900,0.600),#
c("GO:0000302","response to reactive oxygen species", 0.096,-1.618, 1.005, 4.039,-2.2784,0.942,0.602),#
c("GO:0009791","post-embryonic development", 0.098, 6.683,-3.550, 4.048,-1.0400,0.805,0.606),#
c("GO:0051881","regulation of mitochondrial membrane potential", 0.003,-1.699, 6.373, 2.477,-1.1929,0.875,0.610),#
c("GO:0051187","cofactor catabolic process", 0.531,-2.027,-1.695, 4.781,-5.0487,0.857,0.615),#
c("GO:0006397","mRNA processing", 0.620,-4.822,-0.359, 4.849,-8.9747,0.856,0.621),#
c("GO:0007265","Ras protein signal transduction", 0.221,-2.956, 5.997, 4.402,-2.4889,0.855,0.623),#
c("GO:0010324","membrane invagination", 0.005, 4.607, 6.144, 2.777,-1.5812,0.822,0.623),#
c("GO:0006122","mitochondrial electron transport, ubiquinol to cytochrome c", 0.011,-0.080,-1.282, 3.105,-1.6685,0.925,0.627),#
c("GO:0016339","calcium-dependent cell-cell adhesion", 0.001, 1.439,-0.992, 2.201,-1.0433,0.961,0.632),#
c("GO:0030030","cell projection organization", 0.278, 4.677, 6.193, 4.500,-2.1762,0.754,0.635),#
c("GO:0006559","L-phenylalanine catabolic process", 0.019,-3.253,-4.084, 3.331,-2.2959,0.838,0.636),#
c("GO:0006911","phagocytosis, engulfment", 0.005, 4.011, 6.037, 2.743,-1.0521,0.800,0.646),#
c("GO:0006979","response to oxidative stress", 0.231,-1.317, 0.827, 4.420,-2.0583,0.950,0.646),#
c("GO:0060537","muscle tissue development", 0.036, 7.028,-3.549, 3.618,-1.5332,0.829,0.653),#
c("GO:0050684","regulation of mRNA processing", 0.005,-4.394, 4.770, 2.748,-1.7936,0.831,0.653),#
c("GO:0008064","regulation of actin polymerization or depolymerization", 0.026, 2.387, 7.863, 3.464,-7.1506,0.637,0.655),#
c("GO:0016358","dendrite development", 0.014, 7.794, 1.720, 3.188,-1.3150,0.635,0.658),#
c("GO:0006897","endocytosis", 0.075, 1.131, 3.355, 3.934,-1.4100,0.960,0.660),#
c("GO:0002165","instar larval or pupal development", 0.010, 6.716,-3.572, 3.036,-1.3715,0.823,0.662),#
c("GO:0032268","regulation of cellular protein metabolic process", 0.389,-5.544, 4.690, 4.647,-2.1629,0.775,0.664),#
c("GO:0030163","protein catabolic process", 0.408,-4.836,-1.080, 4.667,-1.3202,0.857,0.670),#
c("GO:0010033","response to organic substance", 0.355,-1.417, 1.182, 4.607,-1.1732,0.949,0.670),#
c("GO:0034220","ion transmembrane transport", 1.198, 0.136, 2.096, 5.135,-2.0607,0.923,0.670),#
c("GO:0006570","tyrosine metabolic process", 0.045,-2.154,-4.133, 3.706,-1.3029,0.876,0.672),#
c("GO:0042554","superoxide anion generation", 0.002, 1.269,-1.060, 2.350,-1.0462,0.957,0.675),#
c("GO:0006119","oxidative phosphorylation", 0.910,-0.125,-1.330, 5.016,-4.2692,0.905,0.680),#
c("GO:0019362","pyridine nucleotide metabolic process", 0.466,-3.592,-4.539, 4.725,-3.9281,0.786,0.682),#
c("GO:0006631","fatty acid metabolic process", 0.734,-2.148,-4.054, 4.923,-1.1916,0.860,0.684),#
c("GO:0007052","mitotic spindle organization", 0.006, 4.749, 6.355, 2.839,-4.1726,0.739,0.688),#
c("GO:0060711","labyrinthine layer development", 0.005, 6.754,-3.633, 2.740,-1.0462,0.819,0.689),#
c("GO:0009109","coenzyme catabolic process", 0.518,-2.422,-2.497, 4.771,-5.2684,0.849,0.689),#
c("GO:0030865","cortical cytoskeleton organization", 0.007, 4.950, 6.686, 2.873,-1.7936,0.757,0.691),#
c("GO:0009208","pyrimidine ribonucleoside triphosphate metabolic process", 0.044,-2.712,-4.135, 3.698,-1.0960,0.830,0.694),#
c("GO:0032989","cellular component morphogenesis", 0.840, 7.542, 2.233, 4.981,-1.0284,0.622,0.695),#
c("GO:0051100","negative regulation of binding", 0.024,-2.219, 5.334, 3.430,-1.0433,0.890,0.699))
revigo.data2<- rbind(c("GO:0006800","oxygen and reactive oxygen species metabolic process", 0.154, 1.858, 0.396, 4.210,-2.0916,0.993,0.000),#
c("GO:0007626"," ", 0.020,-1.112, 1.133, 3.364,-1.6635,0.971,0.000),#
c("GO:0008283","cell proliferation", 0.143, 0.694,-0.161, 4.213,-1.0233,0.993,0.000),#
c("GO:0008380","RNA splicing", 0.170,-4.408,-0.013, 4.287,-10.7570,0.873,0.000),#
c("GO:0016192","vesicle-mediated transport", 0.348, 0.764, 3.164, 4.598,-3.0506,0.963,0.000),#
c("GO:0022610","biological adhesion", 0.544, 1.207, 0.368, 4.792,-2.2067,0.993,0.000),#
c("GO:0055114","oxidation-reduction process",16.676, 1.629, 0.426, 6.279,-6.6635,0.982,0.013),#
c("GO:0030716","oocyte fate determination", 0.001, 6.988,-3.504, 1.949,-2.6073,0.831,0.014),#
c("GO:0035088","establishment or maintenance of apical/basal cell polarity", 0.002, 0.328, 0.023, 2.453,-1.3493,0.967,0.015),#
c("GO:0007163","establishment or maintenance of cell polarity", 0.016, 1.499, 0.542, 3.262,-1.3900,0.971,0.016),#
c("GO:0030029","actin filament-based process", 0.106, 0.178,-0.029, 4.084,-6.2848,0.968,0.019),#
c("GO:0007010","cytoskeleton organization", 0.203, 4.735, 6.336, 4.363,-10.4486,0.734,0.020),#
c("GO:0007017","microtubule-based process", 0.308, 0.566, 0.210, 4.546,-5.2226,0.965,0.021),#
c("GO:0000910","cytokinesis", 0.236, 1.601, 0.587, 4.429,-1.2966,0.966,0.021),#
c("GO:0045454","cell redox homeostasis", 0.541,-2.252, 6.619, 4.790,-4.6421,0.830,0.022),#
c("GO:0007155","cell adhesion", 0.540, 0.897,-0.558, 4.789,-2.3218,0.949,0.024),#
c("GO:0042743","hydrogen peroxide metabolic process", 0.046, 0.049,-0.207, 3.718,-1.8137,0.950,0.035),#
c("GO:0017144","drug metabolic process", 0.079, 1.661, 0.611, 3.954,-1.4425,0.953,0.036),#
c("GO:0015980","energy derivation by oxidation of organic compounds", 4.971, 0.029,-1.557, 5.753,-9.0182,0.887,0.052),#
c("GO:0006518","peptide metabolic process", 0.211, 0.787,-0.160, 4.381,-1.4665,0.950,0.054),#
c("GO:0006084","acetyl-CoA metabolic process", 0.531,-0.875,-1.660, 4.782,-6.2684,0.897,0.060),#
c("GO:0006006","glucose metabolic process", 1.107,-2.536,-4.315, 5.101,-8.4908,0.805,0.065),#
c("GO:0009820","alkaloid metabolic process", 0.004, 0.980,-0.151, 2.614,-2.7758,0.962,0.077),#
c("GO:0051186","cofactor metabolic process", 3.543, 0.040, 0.069, 5.606,-3.3125,0.937,0.077),#
c("GO:0006091","generation of precursor metabolites and energy", 6.142, 0.623,-0.201, 5.845,-18.0615,0.934,0.085),#
c("GO:0043603","cellular amide metabolic process", 0.201,-0.518,-1.157, 4.361,-1.3966,0.926,0.108),#
c("GO:0006890","retrograde vesicle-mediated transport, Golgi to ER", 0.005, 1.319, 3.630, 2.757,-1.6644,0.933,0.176),#
c("GO:0048678","response to axon injury", 0.005,-1.154, 0.732, 2.717,-1.0101,0.968,0.214),#
c("GO:0006090","pyruvate metabolic process", 0.041,-2.007,-3.845, 3.667,-4.3215,0.891,0.227),#
c("GO:0006414","translational elongation", 0.665,-5.221, 0.298, 4.880,-6.7905,0.856,0.251),#
c("GO:0051443","positive regulation of ubiquitin-protein ligase activity", 0.002,-4.697, 4.427, 2.332,-3.1308,0.797,0.259),#
c("GO:0008104","protein localization", 1.847, 0.620, 3.155, 5.323,-2.8214,0.936,0.277),#
c("GO:0001539","ciliary or flagellar motility", 0.387, 0.225, 2.329, 4.645,-2.3615,0.932,0.280),#
c("GO:0010608","posttranscriptional regulation of gene expression", 0.218,-4.398, 5.559, 4.395,-2.4001,0.860,0.289),#
c("GO:0006458","'de novo' protein folding", 0.014,-3.541,-0.418, 3.201,-1.7523,0.904,0.296),#
c("GO:0015985","energy coupled proton transport, down electrochemical gradient", 0.663, 0.574, 2.899, 4.879,-2.4501,0.923,0.297),#
c("GO:0016071","mRNA metabolic process", 0.719,-6.026,-1.368, 4.913,-7.6253,0.876,0.300),#
c("GO:0018149","peptide cross-linking", 0.009,-4.101,-0.343, 3.019,-2.2912,0.901,0.306),#
c("GO:0006818","hydrogen transport", 1.025, 0.901, 3.433, 5.067,-2.3529,0.961,0.312),#
c("GO:0021682","nerve maturation", 0.000, 6.949,-3.836, 1.398,-1.6685,0.841,0.315),#
c("GO:0007264","small GTPase mediated signal transduction", 0.496,-2.983, 6.084, 4.753,-2.5153,0.847,0.320),#
c("GO:0010498","proteasomal protein catabolic process", 0.042,-5.261,-1.329, 3.680,-2.8750,0.847,0.321),#
c("GO:0006558","L-phenylalanine metabolic process", 0.058,-2.232,-4.159, 3.818,-2.1048,0.874,0.323),#
c("GO:0006471","protein ADP-ribosylation", 0.013,-3.683,-0.341, 3.180,-1.0960,0.899,0.339),#
c("GO:0009894","regulation of catabolic process", 0.238,-3.396, 4.831, 4.433,-1.5155,0.836,0.345),#
c("GO:0006108","malate metabolic process", 0.111,-2.053,-3.984, 4.103,-1.3029,0.885,0.346),#
c("GO:0010035","response to inorganic substance", 0.247,-1.386, 1.132, 4.449,-2.4658,0.950,0.350),#
c("GO:0007164","establishment of tissue polarity", 0.004, 6.764,-3.366, 2.685,-1.3497,0.853,0.359),#
c("GO:0009205","purine ribonucleoside triphosphate metabolic process", 4.768,-3.673,-3.935, 5.735,-4.6946,0.775,0.369),#
c("GO:0006749","glutathione metabolic process", 0.072,-2.360,-4.572, 3.915,-1.5837,0.878,0.372),#
c("GO:0006769","nicotinamide metabolic process", 0.000,-1.715,-3.752, 0.954,-2.4131,0.874,0.373),#
c("GO:0006396","RNA processing", 2.591,-5.116,-0.789, 5.470,-1.4256,0.857,0.395),#
c("GO:0007566","embryo implantation", 0.003, 6.449,-3.641, 2.507,-1.6644,0.834,0.397),#
c("GO:0051289","protein homotetramerization", 0.007, 4.930, 6.755, 2.888,-1.7869,0.804,0.403),#
c("GO:0019991","septate junction assembly", 0.000, 4.749, 6.216, 1.690,-1.1969,0.816,0.413),#
c("GO:0006457","protein folding", 0.973,-4.392,-0.306, 5.045,-5.6180,0.875,0.426),#
c("GO:0044087","regulation of cellular component biogenesis", 0.077, 2.289, 7.845, 3.943,-3.2426,0.769,0.428),#
c("GO:0043484","regulation of RNA splicing", 0.006,-4.334, 4.564, 2.846,-1.9392,0.824,0.443),#
c("GO:0001700","embryonic development via the syncytial blastoderm", 0.003, 6.337,-3.379, 2.504,-1.0998,0.832,0.446),#
c("GO:0030721","spectrosome organization", 0.000, 4.817, 6.552, 0.699,-1.6685,0.826,0.450),#
c("GO:0051129","negative regulation of cellular component organization", 0.045, 2.265, 7.425, 3.711,-1.8220,0.737,0.458),#
c("GO:0051340","regulation of ligase activity", 0.003,-2.596, 6.152, 2.598,-2.3526,0.892,0.470),#
c("GO:0035152","regulation of tube architecture, open tracheal system", 0.001, 6.080, 0.005, 2.196,-2.7903,0.745,0.472),#
c("GO:0008340","determination of adult lifespan", 0.009, 6.407,-3.413, 3.035,-1.6606,0.825,0.473),#
c("GO:0006085","acetyl-CoA biosynthetic process", 0.004,-1.213,-1.643, 2.697,-2.2385,0.910,0.474),#
c("GO:0045478","fusome organization", 0.000, 4.829, 6.460, 1.279,-1.6685,0.815,0.484),#
c("GO:0051591","response to cAMP", 0.005,-1.258, 0.746, 2.749,-1.7936,0.959,0.490),#
c("GO:0006213","pyrimidine nucleoside metabolic process", 0.201,-3.187,-4.297, 4.359,-1.4180,0.828,0.495),#
c("GO:0043433","negative regulation of sequence-specific DNA binding transcription factor activity", 0.009,-4.260, 4.614, 2.999,-1.0960,0.817,0.499),#
c("GO:0007276","gamete generation", 0.062, 5.891,-4.046, 3.846,-1.4704,0.848,0.500),#
c("GO:0007444","imaginal disc development", 0.009, 6.446,-3.405, 2.991,-1.7166,0.816,0.504),#
c("GO:0016044","cellular membrane organization", 0.166, 5.067, 6.954, 4.276,-1.6677,0.785,0.505),#
c("GO:0060047","heart contraction", 0.013, 5.819,-3.867, 3.159,-1.1929,0.879,0.508),#
c("GO:0019953","sexual reproduction", 0.086, 3.339,-2.209, 3.990,-1.0008,0.959,0.510),#
c("GO:0051084","'de novo' posttranslational protein folding", 0.014,-3.660,-0.386, 3.194,-1.0462,0.904,0.516),#
c("GO:0048754","branching morphogenesis of a tube", 0.021, 6.380,-3.373, 3.372,-1.3150,0.814,0.526),#
c("GO:0010927","cellular component assembly involved in morphogenesis", 0.019, 7.406, 2.247, 3.332,-1.1170,0.660,0.527),#
c("GO:0006413","translational initiation", 0.337,-5.138, 0.300, 4.584,-1.7656,0.863,0.533),#
c("GO:0001763","morphogenesis of a branching structure", 0.026, 6.478,-3.423, 3.470,-1.3294,0.820,0.537),#
c("GO:0006412","translation", 4.967,-5.423, 0.276, 5.753,-5.2041,0.832,0.538),#
c("GO:0045429","positive regulation of nitric oxide biosynthetic process", 0.004,-2.690, 5.902, 2.619,-1.0462,0.842,0.541),#
c("GO:0009992","cellular water homeostasis", 0.000,-1.437, 6.111, 1.623,-1.6685,0.886,0.541),#
c("GO:0006112","energy reserve metabolic process", 0.129,-0.107,-1.299, 4.169,-1.8918,0.915,0.543),#
c("GO:0007016","cytoskeletal anchoring at plasma membrane", 0.002, 2.191, 7.245, 2.401,-3.1273,0.682,0.560),#
c("GO:0042692","muscle cell differentiation", 0.034, 6.774,-3.330, 3.589,-2.5846,0.785,0.563),#
c("GO:0016052","carbohydrate catabolic process", 1.399,-2.781,-2.512, 5.203,-5.3516,0.867,0.564),#
c("GO:0035317","imaginal disc-derived wing hair organization", 0.001, 7.750, 1.636, 2.004,-1.9392,0.666,0.567),#
c("GO:0051235","maintenance of location", 0.032,-1.949, 6.873, 3.556,-1.9771,0.861,0.584),#
c("GO:0005977","glycogen metabolic process", 0.128,-2.440,-1.665, 4.164,-1.8918,0.840,0.589),#
c("GO:0043933","macromolecular complex subunit organization", 1.085, 4.880, 6.508, 5.092,-2.5019,0.781,0.593),#
c("GO:0042775","mitochondrial ATP synthesis coupled electron transport", 0.315,-0.424,-1.022, 4.555,-2.1471,0.906,0.598),#
c("GO:0044042","glucan metabolic process", 0.249,-2.591,-1.536, 4.452,-1.3150,0.900,0.600),#
c("GO:0000302","response to reactive oxygen species", 0.096,-1.618, 1.005, 4.039,-2.2784,0.942,0.602),#
c("GO:0009791","post-embryonic development", 0.098, 6.683,-3.550, 4.048,-1.0400,0.805,0.606),#
c("GO:0051881","regulation of mitochondrial membrane potential", 0.003,-1.699, 6.373, 2.477,-1.1929,0.875,0.610),#
c("GO:0051187","cofactor catabolic process", 0.531,-2.027,-1.695, 4.781,-5.0487,0.857,0.615),#
c("GO:0006397","mRNA processing", 0.620,-4.822,-0.359, 4.849,-8.9747,0.856,0.621),#
c("GO:0007265","Ras protein signal transduction", 0.221,-2.956, 5.997, 4.402,-2.4889,0.855,0.623),#
c("GO:0010324","membrane invagination", 0.005, 4.607, 6.144, 2.777,-1.5812,0.822,0.623),#
c("GO:0006122","mitochondrial electron transport, ubiquinol to cytochrome c", 0.011,-0.080,-1.282, 3.105,-1.6685,0.925,0.627),#
c("GO:0016339","calcium-dependent cell-cell adhesion", 0.001, 1.439,-0.992, 2.201,-1.0433,0.961,0.632),#
c("GO:0030030","cell projection organization", 0.278, 4.677, 6.193, 4.500,-2.1762,0.754,0.635),#
c("GO:0006559","L-phenylalanine catabolic process", 0.019,-3.253,-4.084, 3.331,-2.2959,0.838,0.636),#
c("GO:0006911","phagocytosis, engulfment", 0.005, 4.011, 6.037, 2.743,-1.0521,0.800,0.646),#
c("GO:0006979","response to oxidative stress", 0.231,-1.317, 0.827, 4.420,-2.0583,0.950,0.646),#
c("GO:0060537","muscle tissue development", 0.036, 7.028,-3.549, 3.618,-1.5332,0.829,0.653),#
c("GO:0050684","regulation of mRNA processing", 0.005,-4.394, 4.770, 2.748,-1.7936,0.831,0.653),#
c("GO:0008064","regulation of actin polymerization or depolymerization", 0.026, 2.387, 7.863, 3.464,-7.1506,0.637,0.655),#
c("GO:0016358","dendrite development", 0.014, 7.794, 1.720, 3.188,-1.3150,0.635,0.658),#
c("GO:0006897","endocytosis", 0.075, 1.131, 3.355, 3.934,-1.4100,0.960,0.660),#
c("GO:0002165","instar larval or pupal development", 0.010, 6.716,-3.572, 3.036,-1.3715,0.823,0.662),#
c("GO:0032268","regulation of cellular protein metabolic process", 0.389,-5.544, 4.690, 4.647,-2.1629,0.775,0.664),#
c("GO:0030163","protein catabolic process", 0.408,-4.836,-1.080, 4.667,-1.3202,0.857,0.670),#
c("GO:0010033","response to organic substance", 0.355,-1.417, 1.182, 4.607,-1.1732,0.949,0.670),#
c("GO:0034220","ion transmembrane transport", 1.198, 0.136, 2.096, 5.135,-2.0607,0.923,0.670),#
c("GO:0006570","tyrosine metabolic process", 0.045,-2.154,-4.133, 3.706,-1.3029,0.876,0.672),#
c("GO:0042554","superoxide anion generation", 0.002, 1.269,-1.060, 2.350,-1.0462,0.957,0.675),#
c("GO:0006119","oxidative phosphorylation", 0.910,-0.125,-1.330, 5.016,-4.2692,0.905,0.680),#
c("GO:0019362","pyridine nucleotide metabolic process", 0.466,-3.592,-4.539, 4.725,-3.9281,0.786,0.682),#
c("GO:0006631","fatty acid metabolic process", 0.734,-2.148,-4.054, 4.923,-1.1916,0.860,0.684),#
c("GO:0007052","mitotic spindle organization", 0.006, 4.749, 6.355, 2.839,-4.1726,0.739,0.688),#
c("GO:0060711","labyrinthine layer development", 0.005, 6.754,-3.633, 2.740,-1.0462,0.819,0.689),#
c("GO:0009109","coenzyme catabolic process", 0.518,-2.422,-2.497, 4.771,-5.2684,0.849,0.689),#
c("GO:0030865","cortical cytoskeleton organization", 0.007, 4.950, 6.686, 2.873,-1.7936,0.757,0.691),#
c("GO:0009208","pyrimidine ribonucleoside triphosphate metabolic process", 0.044,-2.712,-4.135, 3.698,-1.0960,0.830,0.694),#
c("GO:0032989","cellular component morphogenesis", 0.840, 7.542, 2.233, 4.981,-1.0284,0.622,0.695),#
c("GO:0051100","negative regulation of binding", 0.024,-2.219, 5.334, 3.430,-1.0433,0.890,0.699))
revigo.data2<- rbind(c("GO:0006800","oxygen and reactive oxygen species metabolic process", 0.154, 1.858, 0.396, 4.210,-2.0916,0.993,0.000),#
c("GO:0007626"," ", 0.020,-1.112, 1.133, 3.364,-1.6635,0.971,0.000),#
c("GO:0008283","", 0.143, 0.694,-0.161, 4.213,-1.0233,0.993,0.000),#
c("GO:0008380","RNA splicing", 0.170,-4.408,-0.013, 4.287,-10.7570,0.873,0.000),#
c("GO:0016192","", 0.348, 0.764, 3.164, 4.598,-3.0506,0.963,0.000),#
c("GO:0022610","", 0.544, 1.207, 0.368, 4.792,-2.2067,0.993,0.000),#
c("GO:0055114","oxidation-reduction process",16.676, 1.629, 0.426, 6.279,-6.6635,0.982,0.013),#
c("GO:0030716","oocyte fate determination", 0.001, 6.988,-3.504, 1.949,-2.6073,0.831,0.014),#
c("GO:0035088","", 0.002, 0.328, 0.023, 2.453,-1.3493,0.967,0.015),#
c("GO:0007163","", 0.016, 1.499, 0.542, 3.262,-1.3900,0.971,0.016),#
c("GO:0030029","", 0.106, 0.178,-0.029, 4.084,-6.2848,0.968,0.019),#
c("GO:0007010","cytoskeleton organization", 0.203, 4.735, 6.336, 4.363,-10.4486,0.734,0.020),#
c("GO:0007017","", 0.308, 0.566, 0.210, 4.546,-5.2226,0.965,0.021),#
c("GO:0000910","", 0.236, 1.601, 0.587, 4.429,-1.2966,0.966,0.021),#
c("GO:0045454","", 0.541,-2.252, 6.619, 4.790,-4.6421,0.830,0.022),#
c("GO:0007155","cell adhesion", 0.540, 0.897,-0.558, 4.789,-2.3218,0.949,0.024),#
c("GO:0042743","", 0.046, 0.049,-0.207, 3.718,-1.8137,0.950,0.035),#
c("GO:0017144","", 0.079, 1.661, 0.611, 3.954,-1.4425,0.953,0.036),#
c("GO:0015980","", 4.971, 0.029,-1.557, 5.753,-9.0182,0.887,0.052),#
c("GO:0006518","peptide metabolic process", 0.211, 0.787,-0.160, 4.381,-1.4665,0.950,0.054),#
c("GO:0006084","", 0.531,-0.875,-1.660, 4.782,-6.2684,0.897,0.060),#
c("GO:0006006","glucose metabolic process", 1.107,-2.536,-4.315, 5.101,-8.4908,0.805,0.065),#
c("GO:0009820","", 0.004, 0.980,-0.151, 2.614,-2.7758,0.962,0.077),#
c("GO:0051186","", 3.543, 0.040, 0.069, 5.606,-3.3125,0.937,0.077),#
c("GO:0006091","", 6.142, 0.623,-0.201, 5.845,-18.0615,0.934,0.085),#
c("GO:0043603","", 0.201,-0.518,-1.157, 4.361,-1.3966,0.926,0.108),#
c("GO:0006890","", 0.005, 1.319, 3.630, 2.757,-1.6644,0.933,0.176),#
c("GO:0048678","", 0.005,-1.154, 0.732, 2.717,-1.0101,0.968,0.214),#
c("GO:0006090","", 0.041,-2.007,-3.845, 3.667,-4.3215,0.891,0.227),#
c("GO:0006414","", 0.665,-5.221, 0.298, 4.880,-6.7905,0.856,0.251),#
c("GO:0051443","", 0.002,-4.697, 4.427, 2.332,-3.1308,0.797,0.259),#
c("GO:0008104","", 1.847, 0.620, 3.155, 5.323,-2.8214,0.936,0.277),#
c("GO:0001539","", 0.387, 0.225, 2.329, 4.645,-2.3615,0.932,0.280),#
c("GO:0010608","", 0.218,-4.398, 5.559, 4.395,-2.4001,0.860,0.289),#
c("GO:0006458","'de novo' protein folding", 0.014,-3.541,-0.418, 3.201,-1.7523,0.904,0.296),#
c("GO:0015985","", 0.663, 0.574, 2.899, 4.879,-2.4501,0.923,0.297),#
c("GO:0016071","", 0.719,-6.026,-1.368, 4.913,-7.6253,0.876,0.300),#
c("GO:0018149","", 0.009,-4.101,-0.343, 3.019,-2.2912,0.901,0.306),#
c("GO:0006818","hydrogen transport", 1.025, 0.901, 3.433, 5.067,-2.3529,0.961,0.312),#
c("GO:0021682","", 0.000, 6.949,-3.836, 1.398,-1.6685,0.841,0.315),#
c("GO:0007264","", 0.496,-2.983, 6.084, 4.753,-2.5153,0.847,0.320),#
c("GO:0010498","", 0.042,-5.261,-1.329, 3.680,-2.8750,0.847,0.321),#
c("GO:0006558","", 0.058,-2.232,-4.159, 3.818,-2.1048,0.874,0.323),#
c("GO:0006471","", 0.013,-3.683,-0.341, 3.180,-1.0960,0.899,0.339),#
c("GO:0009894","", 0.238,-3.396, 4.831, 4.433,-1.5155,0.836,0.345),#
c("GO:0006108","", 0.111,-2.053,-3.984, 4.103,-1.3029,0.885,0.346),#
c("GO:0010035","response to inorganic substance", 0.247,-1.386, 1.132, 4.449,-2.4658,0.950,0.350),#
c("GO:0007164","", 0.004, 6.764,-3.366, 2.685,-1.3497,0.853,0.359),#
c("GO:0009205","", 4.768,-3.673,-3.935, 5.735,-4.6946,0.775,0.369),#
c("GO:0006749","", 0.072,-2.360,-4.572, 3.915,-1.5837,0.878,0.372),#
c("GO:0006769","", 0.000,-1.715,-3.752, 0.954,-2.4131,0.874,0.373),#
c("GO:0006396","RNA processing", 2.591,-5.116,-0.789, 5.470,-1.4256,0.857,0.395),#
c("GO:0007566","", 0.003, 6.449,-3.641, 2.507,-1.6644,0.834,0.397),#
c("GO:0051289","", 0.007, 4.930, 6.755, 2.888,-1.7869,0.804,0.403),#
c("GO:0019991","", 0.000, 4.749, 6.216, 1.690,-1.1969,0.816,0.413),#
c("GO:0006457","protein folding", 0.973,-4.392,-0.306, 5.045,-5.6180,0.875,0.426),#
c("GO:0044087","", 0.077, 2.289, 7.845, 3.943,-3.2426,0.769,0.428),#
c("GO:0043484","regulation of RNA splicing", 0.006,-4.334, 4.564, 2.846,-1.9392,0.824,0.443),#
c("GO:0001700","", 0.003, 6.337,-3.379, 2.504,-1.0998,0.832,0.446),#
c("GO:0030721","", 0.000, 4.817, 6.552, 0.699,-1.6685,0.826,0.450),#
c("GO:0051129","", 0.045, 2.265, 7.425, 3.711,-1.8220,0.737,0.458),#
c("GO:0051340","", 0.003,-2.596, 6.152, 2.598,-2.3526,0.892,0.470),#
c("GO:0035152","", 0.001, 6.080, 0.005, 2.196,-2.7903,0.745,0.472),#
c("GO:0008340","", 0.009, 6.407,-3.413, 3.035,-1.6606,0.825,0.473),#
c("GO:0006085","", 0.004,-1.213,-1.643, 2.697,-2.2385,0.910,0.474),#
c("GO:0045478","", 0.000, 4.829, 6.460, 1.279,-1.6685,0.815,0.484),#
c("GO:0051591","", 0.005,-1.258, 0.746, 2.749,-1.7936,0.959,0.490),#
c("GO:0006213","", 0.201,-3.187,-4.297, 4.359,-1.4180,0.828,0.495),#
c("GO:0043433","", 0.009,-4.260, 4.614, 2.999,-1.0960,0.817,0.499),#
c("GO:0007276","", 0.062, 5.891,-4.046, 3.846,-1.4704,0.848,0.500),#
c("GO:0007444","", 0.009, 6.446,-3.405, 2.991,-1.7166,0.816,0.504),#
c("GO:0016044","", 0.166, 5.067, 6.954, 4.276,-1.6677,0.785,0.505),#
c("GO:0060047","", 0.013, 5.819,-3.867, 3.159,-1.1929,0.879,0.508),#
c("GO:0019953","", 0.086, 3.339,-2.209, 3.990,-1.0008,0.959,0.510),#
c("GO:0051084","", 0.014,-3.660,-0.386, 3.194,-1.0462,0.904,0.516),#
c("GO:0048754","", 0.021, 6.380,-3.373, 3.372,-1.3150,0.814,0.526),#
c("GO:0010927","", 0.019, 7.406, 2.247, 3.332,-1.1170,0.660,0.527),#
c("GO:0006413","", 0.337,-5.138, 0.300, 4.584,-1.7656,0.863,0.533),#
c("GO:0001763","", 0.026, 6.478,-3.423, 3.470,-1.3294,0.820,0.537),#
c("GO:0006412","translation", 4.967,-5.423, 0.276, 5.753,-5.2041,0.832,0.538),#
c("GO:0045429","", 0.004,-2.690, 5.902, 2.619,-1.0462,0.842,0.541),#
c("GO:0009992","", 0.000,-1.437, 6.111, 1.623,-1.6685,0.886,0.541),#
c("GO:0006112","", 0.129,-0.107,-1.299, 4.169,-1.8918,0.915,0.543),#
c("GO:0007016","", 0.002, 2.191, 7.245, 2.401,-3.1273,0.682,0.560),#
c("GO:0042692","", 0.034, 6.774,-3.330, 3.589,-2.5846,0.785,0.563),#
c("GO:0016052","", 1.399,-2.781,-2.512, 5.203,-5.3516,0.867,0.564),#
c("GO:0035317","", 0.001, 7.750, 1.636, 2.004,-1.9392,0.666,0.567),#
c("GO:0051235","", 0.032,-1.949, 6.873, 3.556,-1.9771,0.861,0.584),#
c("GO:0005977","", 0.128,-2.440,-1.665, 4.164,-1.8918,0.840,0.589),#
c("GO:0043933","", 1.085, 4.880, 6.508, 5.092,-2.5019,0.781,0.593),#
c("GO:0042775","", 0.315,-0.424,-1.022, 4.555,-2.1471,0.906,0.598),#
c("GO:0044042","", 0.249,-2.591,-1.536, 4.452,-1.3150,0.900,0.600),#
c("GO:0000302","response to reactive oxygen species", 0.096,-1.618, 1.005, 4.039,-2.2784,0.942,0.602),#
c("GO:0009791","", 0.098, 6.683,-3.550, 4.048,-1.0400,0.805,0.606),#
c("GO:0051881","", 0.003,-1.699, 6.373, 2.477,-1.1929,0.875,0.610),#
c("GO:0051187","", 0.531,-2.027,-1.695, 4.781,-5.0487,0.857,0.615),#
c("GO:0006397","", 0.620,-4.822,-0.359, 4.849,-8.9747,0.856,0.621),#
c("GO:0007265","", 0.221,-2.956, 5.997, 4.402,-2.4889,0.855,0.623),#
c("GO:0010324","", 0.005, 4.607, 6.144, 2.777,-1.5812,0.822,0.623),#
c("GO:0006122","", 0.011,-0.080,-1.282, 3.105,-1.6685,0.925,0.627),#
c("GO:0016339","", 0.001, 1.439,-0.992, 2.201,-1.0433,0.961,0.632),#
c("GO:0030030","", 0.278, 4.677, 6.193, 4.500,-2.1762,0.754,0.635),#
c("GO:0006559","", 0.019,-3.253,-4.084, 3.331,-2.2959,0.838,0.636),#
c("GO:0006911","", 0.005, 4.011, 6.037, 2.743,-1.0521,0.800,0.646),#
c("GO:0006979","response to oxidative stress", 0.231,-1.317, 0.827, 4.420,-2.0583,0.950,0.646),#
c("GO:0060537","muscle tissue development", 0.036, 7.028,-3.549, 3.618,-1.5332,0.829,0.653),#
c("GO:0050684","", 0.005,-4.394, 4.770, 2.748,-1.7936,0.831,0.653),#
c("GO:0008064","", 0.026, 2.387, 7.863, 3.464,-7.1506,0.637,0.655),#
c("GO:0016358","", 0.014, 7.794, 1.720, 3.188,-1.3150,0.635,0.658),#
c("GO:0006897","endocytosis", 0.075, 1.131, 3.355, 3.934,-1.4100,0.960,0.660),#
c("GO:0002165","", 0.010, 6.716,-3.572, 3.036,-1.3715,0.823,0.662),#
c("GO:0032268","", 0.389,-5.544, 4.690, 4.647,-2.1629,0.775,0.664),#
c("GO:0030163","", 0.408,-4.836,-1.080, 4.667,-1.3202,0.857,0.670),#
c("GO:0010033","", 0.355,-1.417, 1.182, 4.607,-1.1732,0.949,0.670),#
c("GO:0034220","", 1.198, 0.136, 2.096, 5.135,-2.0607,0.923,0.670),#
c("GO:0006570","", 0.045,-2.154,-4.133, 3.706,-1.3029,0.876,0.672),#
c("GO:0042554","", 0.002, 1.269,-1.060, 2.350,-1.0462,0.957,0.675),#
c("GO:0006119","", 0.910,-0.125,-1.330, 5.016,-4.2692,0.905,0.680),#
c("GO:0019362","", 0.466,-3.592,-4.539, 4.725,-3.9281,0.786,0.682),#
c("GO:0006631","", 0.734,-2.148,-4.054, 4.923,-1.1916,0.860,0.684),#
c("GO:0007052","", 0.006, 4.749, 6.355, 2.839,-4.1726,0.739,0.688),#
c("GO:0060711","", 0.005, 6.754,-3.633, 2.740,-1.0462,0.819,0.689),#
c("GO:0009109","", 0.518,-2.422,-2.497, 4.771,-5.2684,0.849,0.689),#
c("GO:0030865","", 0.007, 4.950, 6.686, 2.873,-1.7936,0.757,0.691),#
c("GO:0009208","", 0.044,-2.712,-4.135, 3.698,-1.0960,0.830,0.694),#
c("GO:0032989","", 0.840, 7.542, 2.233, 4.981,-1.0284,0.622,0.695),#
c("GO:0051100","", 0.024,-2.219, 5.334, 3.430,-1.0433,0.890,0.699))
one.data <- data.frame(revigo.data2);#
names(one.data) <- revigo.names;#
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];#
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );#
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );#
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );#
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );#
one.data$frequency <- as.numeric( as.character(one.data$frequency) );#
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );#
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) );#
#
p1 <- ggplot( data = one.data );#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );#
ex <- one.data [ one.data$dispensability < 0.15, ]; #
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");#
p1 <- p1 + opts(legend.key = theme_blank()) ;#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10)
p1
revigo.data2<- rbind(c("GO:0006800","", 0.154, 1.858, 0.396, 4.210,-2.0916,0.993,0.000),#
c("GO:0007626"," ", 0.020,-1.112, 1.133, 3.364,-1.6635,0.971,0.000),#
c("GO:0008283","", 0.143, 0.694,-0.161, 4.213,-1.0233,0.993,0.000),#
c("GO:0008380","RNA splicing", 0.170,-4.408,-0.013, 4.287,-10.7570,0.873,0.000),#
c("GO:0016192","vesicle-mediated transport", 0.348, 0.764, 3.164, 4.598,-3.0506,0.963,0.000),#
c("GO:0022610","", 0.544, 1.207, 0.368, 4.792,-2.2067,0.993,0.000),#
c("GO:0055114","",16.676, 1.629, 0.426, 6.279,-6.6635,0.982,0.013),#
c("GO:0030716","oocyte fate determination", 0.001, 6.988,-3.504, 1.949,-2.6073,0.831,0.014),#
c("GO:0035088","", 0.002, 0.328, 0.023, 2.453,-1.3493,0.967,0.015),#
c("GO:0007163","", 0.016, 1.499, 0.542, 3.262,-1.3900,0.971,0.016),#
c("GO:0030029","", 0.106, 0.178,-0.029, 4.084,-6.2848,0.968,0.019),#
c("GO:0007010","cytoskeleton organization", 0.203, 4.735, 6.336, 4.363,-10.4486,0.734,0.020),#
c("GO:0007017","", 0.308, 0.566, 0.210, 4.546,-5.2226,0.965,0.021),#
c("GO:0000910","", 0.236, 1.601, 0.587, 4.429,-1.2966,0.966,0.021),#
c("GO:0045454","", 0.541,-2.252, 6.619, 4.790,-4.6421,0.830,0.022),#
c("GO:0007155","", 0.540, 0.897,-0.558, 4.789,-2.3218,0.949,0.024),#
c("GO:0042743","", 0.046, 0.049,-0.207, 3.718,-1.8137,0.950,0.035),#
c("GO:0017144","", 0.079, 1.661, 0.611, 3.954,-1.4425,0.953,0.036),#
c("GO:0015980","", 4.971, 0.029,-1.557, 5.753,-9.0182,0.887,0.052),#
c("GO:0006518","peptide metabolic process", 0.211, 0.787,-0.160, 4.381,-1.4665,0.950,0.054),#
c("GO:0006084","", 0.531,-0.875,-1.660, 4.782,-6.2684,0.897,0.060),#
c("GO:0006006","glucose metabolic process", 1.107,-2.536,-4.315, 5.101,-8.4908,0.805,0.065),#
c("GO:0009820","", 0.004, 0.980,-0.151, 2.614,-2.7758,0.962,0.077),#
c("GO:0051186","", 3.543, 0.040, 0.069, 5.606,-3.3125,0.937,0.077),#
c("GO:0006091","", 6.142, 0.623,-0.201, 5.845,-18.0615,0.934,0.085),#
c("GO:0043603","", 0.201,-0.518,-1.157, 4.361,-1.3966,0.926,0.108),#
c("GO:0006890","", 0.005, 1.319, 3.630, 2.757,-1.6644,0.933,0.176),#
c("GO:0048678","", 0.005,-1.154, 0.732, 2.717,-1.0101,0.968,0.214),#
c("GO:0006090","", 0.041,-2.007,-3.845, 3.667,-4.3215,0.891,0.227),#
c("GO:0006414","", 0.665,-5.221, 0.298, 4.880,-6.7905,0.856,0.251),#
c("GO:0051443","", 0.002,-4.697, 4.427, 2.332,-3.1308,0.797,0.259),#
c("GO:0008104","", 1.847, 0.620, 3.155, 5.323,-2.8214,0.936,0.277),#
c("GO:0001539","", 0.387, 0.225, 2.329, 4.645,-2.3615,0.932,0.280),#
c("GO:0010608","", 0.218,-4.398, 5.559, 4.395,-2.4001,0.860,0.289),#
c("GO:0006458","", 0.014,-3.541,-0.418, 3.201,-1.7523,0.904,0.296),#
c("GO:0015985","", 0.663, 0.574, 2.899, 4.879,-2.4501,0.923,0.297),#
c("GO:0016071","", 0.719,-6.026,-1.368, 4.913,-7.6253,0.876,0.300),#
c("GO:0018149","", 0.009,-4.101,-0.343, 3.019,-2.2912,0.901,0.306),#
c("GO:0006818","", 1.025, 0.901, 3.433, 5.067,-2.3529,0.961,0.312),#
c("GO:0021682","", 0.000, 6.949,-3.836, 1.398,-1.6685,0.841,0.315),#
c("GO:0007264","", 0.496,-2.983, 6.084, 4.753,-2.5153,0.847,0.320),#
c("GO:0010498","", 0.042,-5.261,-1.329, 3.680,-2.8750,0.847,0.321),#
c("GO:0006558","", 0.058,-2.232,-4.159, 3.818,-2.1048,0.874,0.323),#
c("GO:0006471","", 0.013,-3.683,-0.341, 3.180,-1.0960,0.899,0.339),#
c("GO:0009894","", 0.238,-3.396, 4.831, 4.433,-1.5155,0.836,0.345),#
c("GO:0006108","", 0.111,-2.053,-3.984, 4.103,-1.3029,0.885,0.346),#
c("GO:0010035","", 0.247,-1.386, 1.132, 4.449,-2.4658,0.950,0.350),#
c("GO:0007164","", 0.004, 6.764,-3.366, 2.685,-1.3497,0.853,0.359),#
c("GO:0009205","", 4.768,-3.673,-3.935, 5.735,-4.6946,0.775,0.369),#
c("GO:0006749","", 0.072,-2.360,-4.572, 3.915,-1.5837,0.878,0.372),#
c("GO:0006769","", 0.000,-1.715,-3.752, 0.954,-2.4131,0.874,0.373),#
c("GO:0006396","", 2.591,-5.116,-0.789, 5.470,-1.4256,0.857,0.395),#
c("GO:0007566","", 0.003, 6.449,-3.641, 2.507,-1.6644,0.834,0.397),#
c("GO:0051289","", 0.007, 4.930, 6.755, 2.888,-1.7869,0.804,0.403),#
c("GO:0019991","", 0.000, 4.749, 6.216, 1.690,-1.1969,0.816,0.413),#
c("GO:0006457","", 0.973,-4.392,-0.306, 5.045,-5.6180,0.875,0.426),#
c("GO:0044087","regulation of cellular component biogenesis", 0.077, 2.289, 7.845, 3.943,-3.2426,0.769,0.428),#
c("GO:0043484","regulation of RNA splicing", 0.006,-4.334, 4.564, 2.846,-1.9392,0.824,0.443),#
c("GO:0001700","", 0.003, 6.337,-3.379, 2.504,-1.0998,0.832,0.446),#
c("GO:0030721","", 0.000, 4.817, 6.552, 0.699,-1.6685,0.826,0.450),#
c("GO:0051129","", 0.045, 2.265, 7.425, 3.711,-1.8220,0.737,0.458),#
c("GO:0051340","", 0.003,-2.596, 6.152, 2.598,-2.3526,0.892,0.470),#
c("GO:0035152","", 0.001, 6.080, 0.005, 2.196,-2.7903,0.745,0.472),#
c("GO:0008340","", 0.009, 6.407,-3.413, 3.035,-1.6606,0.825,0.473),#
c("GO:0006085","", 0.004,-1.213,-1.643, 2.697,-2.2385,0.910,0.474),#
c("GO:0045478","", 0.000, 4.829, 6.460, 1.279,-1.6685,0.815,0.484),#
c("GO:0051591","", 0.005,-1.258, 0.746, 2.749,-1.7936,0.959,0.490),#
c("GO:0006213","", 0.201,-3.187,-4.297, 4.359,-1.4180,0.828,0.495),#
c("GO:0043433","", 0.009,-4.260, 4.614, 2.999,-1.0960,0.817,0.499),#
c("GO:0007276","", 0.062, 5.891,-4.046, 3.846,-1.4704,0.848,0.500),#
c("GO:0007444","", 0.009, 6.446,-3.405, 2.991,-1.7166,0.816,0.504),#
c("GO:0016044","", 0.166, 5.067, 6.954, 4.276,-1.6677,0.785,0.505),#
c("GO:0060047","", 0.013, 5.819,-3.867, 3.159,-1.1929,0.879,0.508),#
c("GO:0019953","", 0.086, 3.339,-2.209, 3.990,-1.0008,0.959,0.510),#
c("GO:0051084","", 0.014,-3.660,-0.386, 3.194,-1.0462,0.904,0.516),#
c("GO:0048754","", 0.021, 6.380,-3.373, 3.372,-1.3150,0.814,0.526),#
c("GO:0010927","", 0.019, 7.406, 2.247, 3.332,-1.1170,0.660,0.527),#
c("GO:0006413","", 0.337,-5.138, 0.300, 4.584,-1.7656,0.863,0.533),#
c("GO:0001763","", 0.026, 6.478,-3.423, 3.470,-1.3294,0.820,0.537),#
c("GO:0006412","", 4.967,-5.423, 0.276, 5.753,-5.2041,0.832,0.538),#
c("GO:0045429","", 0.004,-2.690, 5.902, 2.619,-1.0462,0.842,0.541),#
c("GO:0009992","", 0.000,-1.437, 6.111, 1.623,-1.6685,0.886,0.541),#
c("GO:0006112","energy reserve metabolic process", 0.129,-0.107,-1.299, 4.169,-1.8918,0.915,0.543),#
c("GO:0007016","", 0.002, 2.191, 7.245, 2.401,-3.1273,0.682,0.560),#
c("GO:0042692","", 0.034, 6.774,-3.330, 3.589,-2.5846,0.785,0.563),#
c("GO:0016052","", 1.399,-2.781,-2.512, 5.203,-5.3516,0.867,0.564),#
c("GO:0035317","", 0.001, 7.750, 1.636, 2.004,-1.9392,0.666,0.567),#
c("GO:0051235","", 0.032,-1.949, 6.873, 3.556,-1.9771,0.861,0.584),#
c("GO:0005977","glycogen metabolic process", 0.128,-2.440,-1.665, 4.164,-1.8918,0.840,0.589),#
c("GO:0043933","", 1.085, 4.880, 6.508, 5.092,-2.5019,0.781,0.593),#
c("GO:0042775","", 0.315,-0.424,-1.022, 4.555,-2.1471,0.906,0.598),#
c("GO:0044042","", 0.249,-2.591,-1.536, 4.452,-1.3150,0.900,0.600),#
c("GO:0000302","response to reactive oxygen species", 0.096,-1.618, 1.005, 4.039,-2.2784,0.942,0.602),#
c("GO:0009791","", 0.098, 6.683,-3.550, 4.048,-1.0400,0.805,0.606),#
c("GO:0051881","", 0.003,-1.699, 6.373, 2.477,-1.1929,0.875,0.610),#
c("GO:0051187","", 0.531,-2.027,-1.695, 4.781,-5.0487,0.857,0.615),#
c("GO:0006397","mRNA processing", 0.620,-4.822,-0.359, 4.849,-8.9747,0.856,0.621),#
c("GO:0007265","Ras protein signal transduction", 0.221,-2.956, 5.997, 4.402,-2.4889,0.855,0.623),#
c("GO:0010324","", 0.005, 4.607, 6.144, 2.777,-1.5812,0.822,0.623),#
c("GO:0006122","", 0.011,-0.080,-1.282, 3.105,-1.6685,0.925,0.627),#
c("GO:0016339","", 0.001, 1.439,-0.992, 2.201,-1.0433,0.961,0.632),#
c("GO:0030030","", 0.278, 4.677, 6.193, 4.500,-2.1762,0.754,0.635),#
c("GO:0006559","", 0.019,-3.253,-4.084, 3.331,-2.2959,0.838,0.636),#
c("GO:0006911","", 0.005, 4.011, 6.037, 2.743,-1.0521,0.800,0.646),#
c("GO:0006979","", 0.231,-1.317, 0.827, 4.420,-2.0583,0.950,0.646),#
c("GO:0060537","", 0.036, 7.028,-3.549, 3.618,-1.5332,0.829,0.653),#
c("GO:0050684","regulation of mRNA processing", 0.005,-4.394, 4.770, 2.748,-1.7936,0.831,0.653),#
c("GO:0008064","", 0.026, 2.387, 7.863, 3.464,-7.1506,0.637,0.655),#
c("GO:0016358","", 0.014, 7.794, 1.720, 3.188,-1.3150,0.635,0.658),#
c("GO:0006897","endocytosis", 0.075, 1.131, 3.355, 3.934,-1.4100,0.960,0.660),#
c("GO:0002165","", 0.010, 6.716,-3.572, 3.036,-1.3715,0.823,0.662),#
c("GO:0032268","", 0.389,-5.544, 4.690, 4.647,-2.1629,0.775,0.664),#
c("GO:0030163","", 0.408,-4.836,-1.080, 4.667,-1.3202,0.857,0.670),#
c("GO:0010033","", 0.355,-1.417, 1.182, 4.607,-1.1732,0.949,0.670),#
c("GO:0034220","", 1.198, 0.136, 2.096, 5.135,-2.0607,0.923,0.670),#
c("GO:0006570","", 0.045,-2.154,-4.133, 3.706,-1.3029,0.876,0.672),#
c("GO:0042554","", 0.002, 1.269,-1.060, 2.350,-1.0462,0.957,0.675),#
c("GO:0006119","", 0.910,-0.125,-1.330, 5.016,-4.2692,0.905,0.680),#
c("GO:0019362","", 0.466,-3.592,-4.539, 4.725,-3.9281,0.786,0.682),#
c("GO:0006631","", 0.734,-2.148,-4.054, 4.923,-1.1916,0.860,0.684),#
c("GO:0007052","", 0.006, 4.749, 6.355, 2.839,-4.1726,0.739,0.688),#
c("GO:0060711","", 0.005, 6.754,-3.633, 2.740,-1.0462,0.819,0.689),#
c("GO:0009109","", 0.518,-2.422,-2.497, 4.771,-5.2684,0.849,0.689),#
c("GO:0030865","", 0.007, 4.950, 6.686, 2.873,-1.7936,0.757,0.691),#
c("GO:0009208","", 0.044,-2.712,-4.135, 3.698,-1.0960,0.830,0.694),#
c("GO:0032989","cellular component morphogenesis", 0.840, 7.542, 2.233, 4.981,-1.0284,0.622,0.695),#
c("GO:0051100","", 0.024,-2.219, 5.334, 3.430,-1.0433,0.890,0.699))
one.data <- data.frame(revigo.data2);#
names(one.data) <- revigo.names;#
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];#
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );#
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );#
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );#
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );#
one.data$frequency <- as.numeric( as.character(one.data$frequency) );#
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );#
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) );#
#
p1 <- ggplot( data = one.data );#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );#
ex <- one.data [ one.data$dispensability < 0.15, ]; #
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");#
p1 <- p1 + opts(legend.key = theme_blank()) ;#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10)
p1
one.data <- data.frame(revigo.data);
#
names(one.data) <- revigo.names;
#
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];
#
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );
#
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );
#
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );
#
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );
#
one.data$frequency <- as.numeric( as.character(one.data$frequency) );
#
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );
#
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) )
p1 <- ggplot( data = one.data );
#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();
#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );
#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();
#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );
#
ex <- one.data [ one.data$dispensability < 0.15, ]; 
#
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );
#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");
#
p1 <- p1 + opts(legend.key = theme_blank()) ;
#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);
#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);
#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);
#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10)
p1
revigo.data2<- rbind(c("GO:0006800","", 0.154, 1.858, 0.396, 4.210,-2.0916,0.993,0.000),#
c("GO:0007626"," ", 0.020,-1.112, 1.133, 3.364,-1.6635,0.971,0.000),#
c("GO:0008283","", 0.143, 0.694,-0.161, 4.213,-1.0233,0.993,0.000),#
c("GO:0008380","RNA splicing", 0.170,-4.408,-0.013, 4.287,-10.7570,0.873,0.000),#
c("GO:0016192","vesicle-mediated transport", 0.348, 0.764, 3.164, 4.598,-3.0506,0.963,0.000),#
c("GO:0022610","", 0.544, 1.207, 0.368, 4.792,-2.2067,0.993,0.000),#
c("GO:0055114","",16.676, 1.629, 0.426, 6.279,-6.6635,0.982,0.013),#
c("GO:0030716","oocyte fate determination", 0.001, 6.988,-3.504, 1.949,-2.6073,0.831,0.014),#
c("GO:0035088","", 0.002, 0.328, 0.023, 2.453,-1.3493,0.967,0.015),#
c("GO:0007163","", 0.016, 1.499, 0.542, 3.262,-1.3900,0.971,0.016),#
c("GO:0030029","", 0.106, 0.178,-0.029, 4.084,-6.2848,0.968,0.019),#
c("GO:0007010","cytoskeleton organization", 0.203, 4.735, 6.336, 4.363,-10.4486,0.734,0.020),#
c("GO:0007017","", 0.308, 0.566, 0.210, 4.546,-5.2226,0.965,0.021),#
c("GO:0000910","", 0.236, 1.601, 0.587, 4.429,-1.2966,0.966,0.021),#
c("GO:0045454","cell redox homeostasis", 0.541,-2.252, 6.619, 4.790,-4.6421,0.830,0.022),#
c("GO:0007155","", 0.540, 0.897,-0.558, 4.789,-2.3218,0.949,0.024),#
c("GO:0042743","", 0.046, 0.049,-0.207, 3.718,-1.8137,0.950,0.035),#
c("GO:0017144","", 0.079, 1.661, 0.611, 3.954,-1.4425,0.953,0.036),#
c("GO:0015980","energy derivation by oxidation of organic compounds", 4.971, 0.029,-1.557, 5.753,-9.0182,0.887,0.052),#
c("GO:0006518","peptide metabolic process", 0.211, 0.787,-0.160, 4.381,-1.4665,0.950,0.054),#
c("GO:0006084","", 0.531,-0.875,-1.660, 4.782,-6.2684,0.897,0.060),#
c("GO:0006006","glucose metabolic process", 1.107,-2.536,-4.315, 5.101,-8.4908,0.805,0.065),#
c("GO:0009820","", 0.004, 0.980,-0.151, 2.614,-2.7758,0.962,0.077),#
c("GO:0051186","", 3.543, 0.040, 0.069, 5.606,-3.3125,0.937,0.077),#
c("GO:0006091","", 6.142, 0.623,-0.201, 5.845,-18.0615,0.934,0.085),#
c("GO:0043603","cellular amide metabolic process", 0.201,-0.518,-1.157, 4.361,-1.3966,0.926,0.108),#
c("GO:0006890","", 0.005, 1.319, 3.630, 2.757,-1.6644,0.933,0.176),#
c("GO:0048678","", 0.005,-1.154, 0.732, 2.717,-1.0101,0.968,0.214),#
c("GO:0006090","", 0.041,-2.007,-3.845, 3.667,-4.3215,0.891,0.227),#
c("GO:0006414","", 0.665,-5.221, 0.298, 4.880,-6.7905,0.856,0.251),#
c("GO:0051443","", 0.002,-4.697, 4.427, 2.332,-3.1308,0.797,0.259),#
c("GO:0008104","", 1.847, 0.620, 3.155, 5.323,-2.8214,0.936,0.277),#
c("GO:0001539","", 0.387, 0.225, 2.329, 4.645,-2.3615,0.932,0.280),#
c("GO:0010608","", 0.218,-4.398, 5.559, 4.395,-2.4001,0.860,0.289),#
c("GO:0006458","", 0.014,-3.541,-0.418, 3.201,-1.7523,0.904,0.296),#
c("GO:0015985","", 0.663, 0.574, 2.899, 4.879,-2.4501,0.923,0.297),#
c("GO:0016071","", 0.719,-6.026,-1.368, 4.913,-7.6253,0.876,0.300),#
c("GO:0018149","", 0.009,-4.101,-0.343, 3.019,-2.2912,0.901,0.306),#
c("GO:0006818","", 1.025, 0.901, 3.433, 5.067,-2.3529,0.961,0.312),#
c("GO:0021682","", 0.000, 6.949,-3.836, 1.398,-1.6685,0.841,0.315),#
c("GO:0007264","", 0.496,-2.983, 6.084, 4.753,-2.5153,0.847,0.320),#
c("GO:0010498","", 0.042,-5.261,-1.329, 3.680,-2.8750,0.847,0.321),#
c("GO:0006558","", 0.058,-2.232,-4.159, 3.818,-2.1048,0.874,0.323),#
c("GO:0006471","", 0.013,-3.683,-0.341, 3.180,-1.0960,0.899,0.339),#
c("GO:0009894","", 0.238,-3.396, 4.831, 4.433,-1.5155,0.836,0.345),#
c("GO:0006108","", 0.111,-2.053,-3.984, 4.103,-1.3029,0.885,0.346),#
c("GO:0010035","", 0.247,-1.386, 1.132, 4.449,-2.4658,0.950,0.350),#
c("GO:0007164","", 0.004, 6.764,-3.366, 2.685,-1.3497,0.853,0.359),#
c("GO:0009205","", 4.768,-3.673,-3.935, 5.735,-4.6946,0.775,0.369),#
c("GO:0006749","", 0.072,-2.360,-4.572, 3.915,-1.5837,0.878,0.372),#
c("GO:0006769","", 0.000,-1.715,-3.752, 0.954,-2.4131,0.874,0.373),#
c("GO:0006396","", 2.591,-5.116,-0.789, 5.470,-1.4256,0.857,0.395),#
c("GO:0007566","", 0.003, 6.449,-3.641, 2.507,-1.6644,0.834,0.397),#
c("GO:0051289","", 0.007, 4.930, 6.755, 2.888,-1.7869,0.804,0.403),#
c("GO:0019991","", 0.000, 4.749, 6.216, 1.690,-1.1969,0.816,0.413),#
c("GO:0006457","", 0.973,-4.392,-0.306, 5.045,-5.6180,0.875,0.426),#
c("GO:0044087","regulation of cellular component biogenesis", 0.077, 2.289, 7.845, 3.943,-3.2426,0.769,0.428),#
c("GO:0043484","regulation of RNA splicing", 0.006,-4.334, 4.564, 2.846,-1.9392,0.824,0.443),#
c("GO:0001700","", 0.003, 6.337,-3.379, 2.504,-1.0998,0.832,0.446),#
c("GO:0030721","", 0.000, 4.817, 6.552, 0.699,-1.6685,0.826,0.450),#
c("GO:0051129","", 0.045, 2.265, 7.425, 3.711,-1.8220,0.737,0.458),#
c("GO:0051340","", 0.003,-2.596, 6.152, 2.598,-2.3526,0.892,0.470),#
c("GO:0035152","", 0.001, 6.080, 0.005, 2.196,-2.7903,0.745,0.472),#
c("GO:0008340","", 0.009, 6.407,-3.413, 3.035,-1.6606,0.825,0.473),#
c("GO:0006085","", 0.004,-1.213,-1.643, 2.697,-2.2385,0.910,0.474),#
c("GO:0045478","", 0.000, 4.829, 6.460, 1.279,-1.6685,0.815,0.484),#
c("GO:0051591","", 0.005,-1.258, 0.746, 2.749,-1.7936,0.959,0.490),#
c("GO:0006213","", 0.201,-3.187,-4.297, 4.359,-1.4180,0.828,0.495),#
c("GO:0043433","", 0.009,-4.260, 4.614, 2.999,-1.0960,0.817,0.499),#
c("GO:0007276","", 0.062, 5.891,-4.046, 3.846,-1.4704,0.848,0.500),#
c("GO:0007444","", 0.009, 6.446,-3.405, 2.991,-1.7166,0.816,0.504),#
c("GO:0016044","", 0.166, 5.067, 6.954, 4.276,-1.6677,0.785,0.505),#
c("GO:0060047","", 0.013, 5.819,-3.867, 3.159,-1.1929,0.879,0.508),#
c("GO:0019953","", 0.086, 3.339,-2.209, 3.990,-1.0008,0.959,0.510),#
c("GO:0051084","", 0.014,-3.660,-0.386, 3.194,-1.0462,0.904,0.516),#
c("GO:0048754","", 0.021, 6.380,-3.373, 3.372,-1.3150,0.814,0.526),#
c("GO:0010927","", 0.019, 7.406, 2.247, 3.332,-1.1170,0.660,0.527),#
c("GO:0006413","", 0.337,-5.138, 0.300, 4.584,-1.7656,0.863,0.533),#
c("GO:0001763","", 0.026, 6.478,-3.423, 3.470,-1.3294,0.820,0.537),#
c("GO:0006412","", 4.967,-5.423, 0.276, 5.753,-5.2041,0.832,0.538),#
c("GO:0045429","", 0.004,-2.690, 5.902, 2.619,-1.0462,0.842,0.541),#
c("GO:0009992","", 0.000,-1.437, 6.111, 1.623,-1.6685,0.886,0.541),#
c("GO:0006112","energy reserve metabolic process", 0.129,-0.107,-1.299, 4.169,-1.8918,0.915,0.543),#
c("GO:0007016","", 0.002, 2.191, 7.245, 2.401,-3.1273,0.682,0.560),#
c("GO:0042692","", 0.034, 6.774,-3.330, 3.589,-2.5846,0.785,0.563),#
c("GO:0016052","", 1.399,-2.781,-2.512, 5.203,-5.3516,0.867,0.564),#
c("GO:0035317","", 0.001, 7.750, 1.636, 2.004,-1.9392,0.666,0.567),#
c("GO:0051235","", 0.032,-1.949, 6.873, 3.556,-1.9771,0.861,0.584),#
c("GO:0005977","glycogen metabolic process", 0.128,-2.440,-1.665, 4.164,-1.8918,0.840,0.589),#
c("GO:0043933","", 1.085, 4.880, 6.508, 5.092,-2.5019,0.781,0.593),#
c("GO:0042775","", 0.315,-0.424,-1.022, 4.555,-2.1471,0.906,0.598),#
c("GO:0044042","", 0.249,-2.591,-1.536, 4.452,-1.3150,0.900,0.600),#
c("GO:0000302","response to reactive oxygen species", 0.096,-1.618, 1.005, 4.039,-2.2784,0.942,0.602),#
c("GO:0009791","", 0.098, 6.683,-3.550, 4.048,-1.0400,0.805,0.606),#
c("GO:0051881","", 0.003,-1.699, 6.373, 2.477,-1.1929,0.875,0.610),#
c("GO:0051187","", 0.531,-2.027,-1.695, 4.781,-5.0487,0.857,0.615),#
c("GO:0006397","mRNA processing", 0.620,-4.822,-0.359, 4.849,-8.9747,0.856,0.621),#
c("GO:0007265","Ras protein signal transduction", 0.221,-2.956, 5.997, 4.402,-2.4889,0.855,0.623),#
c("GO:0010324","", 0.005, 4.607, 6.144, 2.777,-1.5812,0.822,0.623),#
c("GO:0006122","", 0.011,-0.080,-1.282, 3.105,-1.6685,0.925,0.627),#
c("GO:0016339","", 0.001, 1.439,-0.992, 2.201,-1.0433,0.961,0.632),#
c("GO:0030030","", 0.278, 4.677, 6.193, 4.500,-2.1762,0.754,0.635),#
c("GO:0006559","", 0.019,-3.253,-4.084, 3.331,-2.2959,0.838,0.636),#
c("GO:0006911","", 0.005, 4.011, 6.037, 2.743,-1.0521,0.800,0.646),#
c("GO:0006979","", 0.231,-1.317, 0.827, 4.420,-2.0583,0.950,0.646),#
c("GO:0060537","", 0.036, 7.028,-3.549, 3.618,-1.5332,0.829,0.653),#
c("GO:0050684","regulation of mRNA processing", 0.005,-4.394, 4.770, 2.748,-1.7936,0.831,0.653),#
c("GO:0008064","", 0.026, 2.387, 7.863, 3.464,-7.1506,0.637,0.655),#
c("GO:0016358","", 0.014, 7.794, 1.720, 3.188,-1.3150,0.635,0.658),#
c("GO:0006897","endocytosis", 0.075, 1.131, 3.355, 3.934,-1.4100,0.960,0.660),#
c("GO:0002165","", 0.010, 6.716,-3.572, 3.036,-1.3715,0.823,0.662),#
c("GO:0032268","", 0.389,-5.544, 4.690, 4.647,-2.1629,0.775,0.664),#
c("GO:0030163","", 0.408,-4.836,-1.080, 4.667,-1.3202,0.857,0.670),#
c("GO:0010033","", 0.355,-1.417, 1.182, 4.607,-1.1732,0.949,0.670),#
c("GO:0034220","", 1.198, 0.136, 2.096, 5.135,-2.0607,0.923,0.670),#
c("GO:0006570","", 0.045,-2.154,-4.133, 3.706,-1.3029,0.876,0.672),#
c("GO:0042554","", 0.002, 1.269,-1.060, 2.350,-1.0462,0.957,0.675),#
c("GO:0006119","", 0.910,-0.125,-1.330, 5.016,-4.2692,0.905,0.680),#
c("GO:0019362","", 0.466,-3.592,-4.539, 4.725,-3.9281,0.786,0.682),#
c("GO:0006631","", 0.734,-2.148,-4.054, 4.923,-1.1916,0.860,0.684),#
c("GO:0007052","", 0.006, 4.749, 6.355, 2.839,-4.1726,0.739,0.688),#
c("GO:0060711","", 0.005, 6.754,-3.633, 2.740,-1.0462,0.819,0.689),#
c("GO:0009109","", 0.518,-2.422,-2.497, 4.771,-5.2684,0.849,0.689),#
c("GO:0030865","", 0.007, 4.950, 6.686, 2.873,-1.7936,0.757,0.691),#
c("GO:0009208","", 0.044,-2.712,-4.135, 3.698,-1.0960,0.830,0.694),#
c("GO:0032989","cellular component morphogenesis", 0.840, 7.542, 2.233, 4.981,-1.0284,0.622,0.695),#
c("GO:0051100","", 0.024,-2.219, 5.334, 3.430,-1.0433,0.890,0.699))
one.data <- data.frame(revigo.data2);#
names(one.data) <- revigo.names;#
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];#
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );#
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );#
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );#
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );#
one.data$frequency <- as.numeric( as.character(one.data$frequency) );#
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );#
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) );#
#
p1 <- ggplot( data = one.data );#
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();#
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );#
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();#
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );#
ex <- one.data [ one.data$dispensability < 0.15, ]; #
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );#
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");#
p1 <- p1 + opts(legend.key = theme_blank()) ;#
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);#
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);#
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);#
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10)
p1
no.peps<-c(1000,5000,10000,12000,500,15000,50000,30000,40000,70000)#
no.prots<-c(587,1344,1773,1864,331,1936,2658,2400,2516,2833)
plot(no.peps, no.prots, xlab="Number of Sequenced Peptides", ylab='Number of Unique Proteins Identified', pch=19)
citation()
source('http://bioconductor.org/biocLite.R')
biocLite('DESeq')
library(lattice)
library(locfit)
biocLite('DESeq')
source('http://bioconductor.org/biocLite.R')
biocLite('DESeq')
source('http://bioconductor.org/biocLite.R')
biocLite('DESeq')
library(vegdist)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/proteomics/DB post-genome/QE analysis")
QE.prot<-read.csv('QE spec counts for DESeq.csv', header=T, row.names=1)
?read.csv
QE.prot<-read.csv('QE spec counts for DESeq.csv', header=T, row.names=T)
QE.prot<-read.csv('QE spec counts for DESeq.csv', header=T, row.names=1)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/proteomics/DB post-genome/OT expression comparison")
pCO2.prot<-read.csv('pCO2 expression for deseq.csv', header=T, row.names=1)
head(pCO2.prot)
proteindesign2 = data.frame(row.names = colnames(QE.prot), condition = c("highco2", "highco2", "highco2", "highco2", "lowco2", "lowco2", "lowco2", "lowco2"), libType = c(rep('single-end', 8)))
head(QE.prot)
QE.prot<-read.csv('QE spec counts for DESeq CO2.csv', header=T, row.names=1)
QE.prot<-read.csv('QE spec counts for DESeq pCO2.csv', header=T, row.names=1)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/proteomics/DB post-genome/QE analysis")
QE.prot<-read.csv('QE spec counts for DESeq pCO2.csv', header=T, row.names=1)
proteindesign2 = data.frame(row.names = colnames(QE.prot), condition = c("highco2", "highco2", "highco2", "highco2", "lowco2", "lowco2", "lowco2", "lowco2"), libType = c(rep('single-end', 8)))
condition = factor(c("highco2", "highco2", "highco2", "highco2", "lowco2", "lowco2", "lowco2", "lowco2"))
cds= newCountDataSet(QE.prot, condition)
library(DESeq)
cds= newCountDataSet(QE.prot, condition)
cds = estimateSizeFacotr(cds)
cds = estimateSizeFactor(cds)
cds = estimateSizeFactors(cds)
sizeFactors(cds)
cds=estimateDispersion(cds)
cds=estimateDispersions(cds)
plotDispEsts(cds)
res=nbinomTest(cds, 'highco2', 'lowco2')
plotMA(res)
hist(res$pval, breaks=100, col='skyblue', border='slateblue', main='')
ResSig=res[res$padj<0.1]
ResSig=res[res$padj<0.1,]
head(resSig[order(resSig$pval),])
head(ResSig[order(resSig$pval),])
head(ResSig[order(ResSig$pval),])
QE.prot<-read.csv('QE spec counts for DESeq.csv', header=T, row.names=1)
QE.prot<-read.csv('QE spec counts for DESeq ambient MS.csv', header=T, row.names=1)
proteindesign2 = data.frame(row.names = colnames(QE.prot), condition = c(rep('NS', 4), rep('MS', 4)), libType = c(rep('single-end', 8)))
condition = factor(c(rep('NS', 4), rep('MS', 4))
)
QE.MS<-read.csv('QE spec counts for DESeq ambient MS.csv', header=T, row.names=1)
proteindesign3 = data.frame(row.names = colnames(QE.MS), condition = c(rep('NS', 4), rep('MS', 4)), libType = c(rep('single-end', 8)))
condition = factor(c(rep('NS', 4), rep('MS', 4)))
cds= newCountDataSet(QE.MS, condition)
cds = estimateSizeFactors(cds)
sizeFactors(cds)
cds=estimateDispersions(cds)
plotDispEsts(cds)
res=nbinomTest(cds, 'NS', 'MS')
plotMA(res)
hist(res$pval, breaks=100, col='skyblue', border='slateblue', main='')
ResSig=res[res$padj<0.1,]
head(ResSig[order(ResSig$pval),])