Nothing
R/save_network.R
In SDDE: Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks
# function save_network
# Save a picture of the augmented network Y with original node in white and
# additional node in orange.
# Input:
# g1: network X
# g2: augmented network Y
# filename: output filename
# Output:
# Two png files. The first one (identified as 1) is the representation of the original network X.
# The second one (identified as 2) is the representation of the augmented network Y.
# version 1.0
# created Etienne Lord
# since December 2014
# Layout: layout.fruchterman.reingold, layout.kamada.kawai
# Color from Kelly KL. Twenty-two colors of maximum contrast. Col Eng 1976;3:26-27. See also :
# http://jfly.iam.u-tokyo.ac.jp/color/, and Campadelli, P., Posenato, R., & Schettini, R. (1999). An algorithm for the selection of high-contrast color sets. Color Research & Application, 24(2), 132-138.
save_network<-function(g1,g2, filename, layout=layout.kamada.kawai, taxnames='', mode='png', imagesize=800) {
#g1 = blue
#g2 = orange
if (mode!="screen") cat("Saving graph [",filename,"]\n");
# Color from Kelly KL. Twenty-two colors of maximum contrast. Col Eng 1976;3:26-27. See also :
# http://jfly.iam.u-tokyo.ac.jp/color/, and Campadelli, P., Posenato, R., & Schettini, R. (1999). An algorithm for the selection of high-contrast color sets. Color Research & Application, 24(2), 132-138.
Kelly_color=c("#FFFFFF","#FFB300","#803E75","#FF6800","#A6BDD7","#C10020","#CEA262","#817066","#007D34","#F6768E","#00538A","#FF7A5C","#53377A","#FF8E00","#B32851","#F4C800","#7F180D","#93AA00","#593315","#F13A13","#232C16","#000000")
nv=c("Original nodes","Augmented nodes"); #name vector
cv=c("white","orange"); #color vector
if (taxnames=='') {
V(g2)$color <- ifelse((V(g2)$name %in% V(g1)$name), "white", "orange");
V(g1)$color <-"white";
} else if (taxnames=='allgroup'&&!is.null(V(g2)$name)&&!is.null(V(g2)$tax)) {
i=1;
nv=c();
cv=c();
cl=Kelly_color;
if (length(table(V(g2)$tax))<10) cl=rainbow(length(table(V(g2)$tax)));
#Create a table of the coloring
for (a in names(table(V(g2)$tax))) {
cv=c(cv,cl[i]);
nv=c(nv,a);
i=i+1;
}
for (i in 1:length(V(g2)$name)) {
color_pos=match(V(g2)[i]$tax, nv);
V(g2)[i]$color=cv[color_pos];
}
for (i in 1:length(V(g1)$name)) {
color_pos=match(V(g1)[i]$tax, nv);
V(g1)[i]$color=cv[color_pos];
}
} else if (taxnames!=''&&taxnames!='allgroup'){
V(g2)$color <- ifelse((V(g2)$tax != taxnames||V(g2)$name!=taxnames), "white", "orange")
V(g1)$color <-"white";
} else {
V(g2)$color <- ifelse((V(g2)$name %in% V(g1)$name), "white", "orange");
V(g1)$color <-"white";
}
V(g2)$size=10;
V(g1)$size=10;
#Unique
vertex_of_g2<-V(g2)[!(V(g2) %in% V(g1))]
vertex_of_g1=length(V(g1)$name)
if (length(V(g2)) > 50) {
save_network_big(g1,g2, filename, layout, taxnames, mode, imagesize);
} else {
if (mode=='png') {
f2<-paste(filename,"_2",".png", sep="");
png(f2, imagesize, imagesize, pointsize = 14);
plot(g2,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g2)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='svg') {
f2<-paste(filename,"_2",".svg", sep="");
svg(f2);
plot(g2,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g2)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='eps'){
f2<-paste(filename,"_2",".eps", sep="");
postscript(f2, horizontal = FALSE, fonts=c("serif", "Palatino"), onefile = FALSE, paper = "special", height = 8, width = 10)
plot(g2,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else {
plot(g2,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
}
#layout=layout, # the layout method. see the igraph documentation for details
if (mode=='png') {
f1<-paste(filename,"_1",".png", sep="");
png(f1, 800, 800, pointsize = 14);
plot(g1,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='svg') {
f1<-paste(filename,"_1",".svg", sep="");
svg(f1);
plot(g1,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='eps') {
f1<-paste(filename,"_1",".eps", sep="");
postscript(f1, fonts=c("serif", "Palatino"),horizontal = FALSE, onefile = FALSE, paper = "special", height = 8, width = 10)
plot(g1,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
}
if (mode!="screen") print("done")
}
}
save_network_big<-function(g1,g2, filename, layout=layout.kamada.kawai, taxnames='', mode='png', imagesize=2500) {
#g1 = white
#g2 = orange
Kelly_color=c("#FFFFFF","#FFB300","#803E75","#FF6800","#A6BDD7","#C10020","#CEA262","#817066","#007D34","#F6768E","#00538A","#FF7A5C","#53377A","#FF8E00","#B32851","#F4C800","#7F180D","#93AA00","#593315","#F13A13","#232C16","#000000")
nv=c("Original nodes","Augmented nodes"); #name vector
cv=c("white","orange"); #color vector
if (taxnames=='') {
V(g2)$color <- ifelse((V(g2)$name %in% V(g1)$name), "white", "orange")
} else if (taxnames=='allgroup'&&!is.null(V(g2)$name)) {
i=1;
nv=c();
cv=c();
cl=Kelly_color;
if (length(table(V(g2)$tax))<10) {
cl=rainbow(length(table(V(g2)$tax)));
# if (length(table(V(g2)$tax))==3) {
# cl[1]="white";
# cl[2]="orange";
# cl[3]="black";
# }
}
#Create a table of the coloring
for (a in names(table(V(g2)$tax))) {
cv=c(cv,cl[i]);
nv=c(nv,a);
i=i+1;
}
for (i in 1:length(V(g2)$name)) {
color_pos=match(V(g2)[i]$tax, nv);
V(g2)[i]$color=cv[color_pos];
}
for (i in 1:length(V(g1)$name)) {
color_pos=match(V(g1)[i]$tax, nv);
V(g1)[i]$color=cv[color_pos];
}
} else if (taxnames!=''&&taxnames!='allgroup'){
V(g2)$color <- ifelse((V(g2)$tax != taxnames||V(g2)$name!=taxnames), "white", "orange")
V(g1)$color <-"white";
} else {
V(g2)$color <- ifelse((V(g2)$name %in% V(g1)$name), "white", "orange");
V(g1)$color <-"white";
}
V(g2)$size=2.5;
V(g1)$size=2.5;
#filename2<-paste("graph_randomy",count,".txt", sep="");
#sink(filename2)
#print(res1);
#print(res2);
#sink()
#layout=layout; # the layout method. see the igraph documentation for details
if (mode=='png') {
f2<-paste(filename,"_2",".png", sep="");
png(f2, imagesize, imagesize, pointsize = 14);
plot(g2,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='svg') {
f2<-paste(filename,"_2",".svg", sep="");
svg(f2);
plot(g2,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='eps') {
f2<-paste(filename,"_2",".eps", sep="");
postscript(f2, , fonts=c("serif", "Palatino"), horizontal = FALSE, onefile = FALSE, paper = "special", height = 8, width = 10)
plot(g2,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
vertex.label.cex=1,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else {
plot(g2,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
vertex.label.cex=1,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
}
if (mode=='png') {
f1<-paste(filename,"_1",".png", sep="");
png(f1, imagesize, imagesize, pointsize = 14);
plot(g1,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='svg') {
f1<-paste(filename,"_1",".svg", sep="");
svg(f1);
plot(g1,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
vertex.label.cex=1,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='eps'){
f1<-paste(filename,"_1",".eps", sep="");
postscript(f1, , fonts=c("serif", "Palatino"), horizontal = FALSE, onefile = FALSE, paper = "special", height = 8, width = 10)
plot(g1,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
vertex.label.cex=1,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
}
if (mode!="screen") print("done")
}
#Wrapper to plot to std output
plot_network<-function(g1,g2,layout=layout.kamada.kawai, taxnames='') {
save_network(g1,g2,filename='dummy',taxnames=taxnames, layout=layout,mode='screen');
}
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# function save_network
# Save a picture of the augmented network Y with original node in white and
# additional node in orange.
# Input:
# g1: network X
# g2: augmented network Y
# filename: output filename
# Output:
# Two png files. The first one (identified as 1) is the representation of the original network X.
# The second one (identified as 2) is the representation of the augmented network Y.
# version 1.0
# created Etienne Lord
# since December 2014
# Layout: layout.fruchterman.reingold, layout.kamada.kawai
# Color from Kelly KL. Twenty-two colors of maximum contrast. Col Eng 1976;3:26-27. See also :
# http://jfly.iam.u-tokyo.ac.jp/color/, and Campadelli, P., Posenato, R., & Schettini, R. (1999). An algorithm for the selection of high-contrast color sets. Color Research & Application, 24(2), 132-138.
save_network<-function(g1,g2, filename, layout=layout.kamada.kawai, taxnames='', mode='png', imagesize=800) {
#g1 = blue
#g2 = orange
if (mode!="screen") cat("Saving graph [",filename,"]\n");
# Color from Kelly KL. Twenty-two colors of maximum contrast. Col Eng 1976;3:26-27. See also :
# http://jfly.iam.u-tokyo.ac.jp/color/, and Campadelli, P., Posenato, R., & Schettini, R. (1999). An algorithm for the selection of high-contrast color sets. Color Research & Application, 24(2), 132-138.
Kelly_color=c("#FFFFFF","#FFB300","#803E75","#FF6800","#A6BDD7","#C10020","#CEA262","#817066","#007D34","#F6768E","#00538A","#FF7A5C","#53377A","#FF8E00","#B32851","#F4C800","#7F180D","#93AA00","#593315","#F13A13","#232C16","#000000")
nv=c("Original nodes","Augmented nodes"); #name vector
cv=c("white","orange"); #color vector
if (taxnames=='') {
V(g2)$color <- ifelse((V(g2)$name %in% V(g1)$name), "white", "orange");
V(g1)$color <-"white";
} else if (taxnames=='allgroup'&&!is.null(V(g2)$name)&&!is.null(V(g2)$tax)) {
i=1;
nv=c();
cv=c();
cl=Kelly_color;
if (length(table(V(g2)$tax))<10) cl=rainbow(length(table(V(g2)$tax)));
#Create a table of the coloring
for (a in names(table(V(g2)$tax))) {
cv=c(cv,cl[i]);
nv=c(nv,a);
i=i+1;
}
for (i in 1:length(V(g2)$name)) {
color_pos=match(V(g2)[i]$tax, nv);
V(g2)[i]$color=cv[color_pos];
}
for (i in 1:length(V(g1)$name)) {
color_pos=match(V(g1)[i]$tax, nv);
V(g1)[i]$color=cv[color_pos];
}
} else if (taxnames!=''&&taxnames!='allgroup'){
V(g2)$color <- ifelse((V(g2)$tax != taxnames||V(g2)$name!=taxnames), "white", "orange")
V(g1)$color <-"white";
} else {
V(g2)$color <- ifelse((V(g2)$name %in% V(g1)$name), "white", "orange");
V(g1)$color <-"white";
}
V(g2)$size=10;
V(g1)$size=10;
#Unique
vertex_of_g2<-V(g2)[!(V(g2) %in% V(g1))]
vertex_of_g1=length(V(g1)$name)
if (length(V(g2)) > 50) {
save_network_big(g1,g2, filename, layout, taxnames, mode, imagesize);
} else {
if (mode=='png') {
f2<-paste(filename,"_2",".png", sep="");
png(f2, imagesize, imagesize, pointsize = 14);
plot(g2,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g2)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='svg') {
f2<-paste(filename,"_2",".svg", sep="");
svg(f2);
plot(g2,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g2)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='eps'){
f2<-paste(filename,"_2",".eps", sep="");
postscript(f2, horizontal = FALSE, fonts=c("serif", "Palatino"), onefile = FALSE, paper = "special", height = 8, width = 10)
plot(g2,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else {
plot(g2,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
}
#layout=layout, # the layout method. see the igraph documentation for details
if (mode=='png') {
f1<-paste(filename,"_1",".png", sep="");
png(f1, 800, 800, pointsize = 14);
plot(g1,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='svg') {
f1<-paste(filename,"_1",".svg", sep="");
svg(f1);
plot(g1,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='eps') {
f1<-paste(filename,"_1",".eps", sep="");
postscript(f1, fonts=c("serif", "Palatino"),horizontal = FALSE, onefile = FALSE, paper = "special", height = 8, width = 10)
plot(g1,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=V(g1)$name #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
}
if (mode!="screen") print("done")
}
}
save_network_big<-function(g1,g2, filename, layout=layout.kamada.kawai, taxnames='', mode='png', imagesize=2500) {
#g1 = white
#g2 = orange
Kelly_color=c("#FFFFFF","#FFB300","#803E75","#FF6800","#A6BDD7","#C10020","#CEA262","#817066","#007D34","#F6768E","#00538A","#FF7A5C","#53377A","#FF8E00","#B32851","#F4C800","#7F180D","#93AA00","#593315","#F13A13","#232C16","#000000")
nv=c("Original nodes","Augmented nodes"); #name vector
cv=c("white","orange"); #color vector
if (taxnames=='') {
V(g2)$color <- ifelse((V(g2)$name %in% V(g1)$name), "white", "orange")
} else if (taxnames=='allgroup'&&!is.null(V(g2)$name)) {
i=1;
nv=c();
cv=c();
cl=Kelly_color;
if (length(table(V(g2)$tax))<10) {
cl=rainbow(length(table(V(g2)$tax)));
# if (length(table(V(g2)$tax))==3) {
# cl[1]="white";
# cl[2]="orange";
# cl[3]="black";
# }
}
#Create a table of the coloring
for (a in names(table(V(g2)$tax))) {
cv=c(cv,cl[i]);
nv=c(nv,a);
i=i+1;
}
for (i in 1:length(V(g2)$name)) {
color_pos=match(V(g2)[i]$tax, nv);
V(g2)[i]$color=cv[color_pos];
}
for (i in 1:length(V(g1)$name)) {
color_pos=match(V(g1)[i]$tax, nv);
V(g1)[i]$color=cv[color_pos];
}
} else if (taxnames!=''&&taxnames!='allgroup'){
V(g2)$color <- ifelse((V(g2)$tax != taxnames||V(g2)$name!=taxnames), "white", "orange")
V(g1)$color <-"white";
} else {
V(g2)$color <- ifelse((V(g2)$name %in% V(g1)$name), "white", "orange");
V(g1)$color <-"white";
}
V(g2)$size=2.5;
V(g1)$size=2.5;
#filename2<-paste("graph_randomy",count,".txt", sep="");
#sink(filename2)
#print(res1);
#print(res2);
#sink()
#layout=layout; # the layout method. see the igraph documentation for details
if (mode=='png') {
f2<-paste(filename,"_2",".png", sep="");
png(f2, imagesize, imagesize, pointsize = 14);
plot(g2,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='svg') {
f2<-paste(filename,"_2",".svg", sep="");
svg(f2);
plot(g2,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='eps') {
f2<-paste(filename,"_2",".eps", sep="");
postscript(f2, , fonts=c("serif", "Palatino"), horizontal = FALSE, onefile = FALSE, paper = "special", height = 8, width = 10)
plot(g2,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
vertex.label.cex=1,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else {
plot(g2,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
vertex.label.cex=1,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
}
if (mode=='png') {
f1<-paste(filename,"_1",".png", sep="");
png(f1, imagesize, imagesize, pointsize = 14);
plot(g1,
layout=layout,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='svg') {
f1<-paste(filename,"_1",".svg", sep="");
svg(f1);
plot(g1,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
vertex.label.cex=1,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
} else if (mode=='eps'){
f1<-paste(filename,"_1",".eps", sep="");
postscript(f1, , fonts=c("serif", "Palatino"), horizontal = FALSE, onefile = FALSE, paper = "special", height = 8, width = 10)
plot(g1,
layout=layout,
vertex.label.family="serif",
edge.label.family="Palatino",
vertex.label.cex=1,
main=filename, #specifies the title
vertex.label.dist=0, #puts the name labels slightly off the dots
vertex.frame.color='black', #the color of the border of the dots
vertex.label.color='black', #the color of the name labels
vertex.label.font=1, #the font of the name labels
vertex.label=NA #specifies the lables of the vertices. in this case the 'name' attribute is used
);
legend(x="bottomright",title="Legend", legend=nv,pt.bg=cv, pt.cex=2, col="black",pch=21, yjust=0, lty=0);
a=dev.off();
}
if (mode!="screen") print("done")
}
#Wrapper to plot to std output
plot_network<-function(g1,g2,layout=layout.kamada.kawai, taxnames='') {
save_network(g1,g2,filename='dummy',taxnames=taxnames, layout=layout,mode='screen');
}
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