R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
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> bundle_rot<-read.table(file.choose())
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 2 did not have 6 elements
> bundle_rot<-read.table(file.choose(),sep="\t",header=TRUE,row.names=1)
> bundle_rot
     Alpha.helical.bundle Beta.barrel.core
1N55             56.19680         235.7242
1KKO             40.12218         177.2380
1E15             50.53102         138.5232
3CH0             75.14403         144.3122
3CWN             65.90367         223.3066
> plot(bundle_rot,xlab="PDB ID.",ylab="Omega[w]")
> plot(bundle_rot,xlab="PDB ID.",ylab=Omega[w])
Error in plot.default(x[[1L]], x[[2L]], xlab = xlab, ylab = ylab, ...) : 
  object 'Omega' not found
> plot(bundle_rot,xlab="PDB ID.",ylab=expression(Omega[w]))
> plot(bundle_rot[,1],xlab="PDB ID.",ylab=expression(Omega[w]))
> plot(bundle_rot[,3],xlab="PDB ID.",ylab=expression(Omega[w]))
Error in `[.data.frame`(bundle_rot, , 3) : undefined columns selected
> plot(bundle_rot[,2],xlab="PDB ID.",ylab=expression(Omega[w]))
> plot(bundle_rot[,2],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250))
> plot(bundle_rot[,1],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250))
> plot(bundle_rot[,2],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red")
> points(bundle_rot[,1],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250))
> bundle_trans<-read.table(file.choose(),sep="\t",header=TRUE,row.names=1)
> plot(bundle_rot[,2],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red")
> points(bundle_rot[,1],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250))
> points(bundle_trans[,1],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),pch=19)
> points(bundle_trans[,2],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),pch=19,col="red")
> plot(bundle_rot[,2],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red",cex=1.5)
> points(bundle_rot[,1],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),cex=1.5)
> psplotfilename="Metric_bundle_rotation_translation.pdf"
> pdf(psplotfilename, height=4, width=3.15,pointsize=10, onefile=FALSE, paper='a4')
> plot(bundle_rot[,2],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red",cex=1.5)
> points(bundle_rot[,1],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250))
> dev.off()
quartz 
     2 
> psplotfilename="Metric_bundle_rotation_translation.pdf"
> pdf(psplotfilename, height=4, width=3.15,pointsize=10, onefile=FALSE, paper='a4',units="in")
Error in pdf(psplotfilename, height = 4, width = 3.15, pointsize = 10,  : 
  unused argument (units = "in")
> psplotfilename="Metric_bundle_rotation_translation.pdf"
> pdf(psplotfilename, height=4, width=2.63,pointsize=10, onefile=FALSE, paper='a4')
> plot(bundle_rot[,2],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red",cex=1.5)
> points(bundle_rot[,1],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250))
> dev.off()
quartz 
     2 
> psplotfilename="Metric_bundle_rotation_translation.pdf"
> pdf(psplotfilename, height=4, width=3.5,pointsize=10, onefile=FALSE, paper='a4')
> plot(bundle_rot[,2],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red",cex=1.5)
> points(bundle_rot[,1],xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250))
> dev.off()
quartz 
     2 
> psplotfilename="Metric_bundle_rotation_translation.eps"
> eps(psplotfilename, height=4, width=3.5,pointsize=10, onefile=FALSE, paper='a4')
Error: could not find function "eps"
> psplotfilename="Metric_bundle_rotation_translation.eps"
> postscript(psplotfilename, height=4, width=3.5,pointsize=10, onefile=FALSE, paper='a4')
> plot(bundle_rot[,2],xaxt="n",xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red",cex=1.5,)
> axis(1,labels=c("1N55","1KKO","1E15","3CH0","3CWN"))
Error in axis(1, labels = c("1N55", "1KKO", "1E15", "3CH0", "3CWN")) : 
  'labels' is supplied and not 'at'
> axis(1,labels=c("1N55","1KKO","1E15","3CH0","3CWN"),at=c(1:5))
> points(bundle_rot[,1])
> points(bundle_trans[,1])
> points(bundle_trans[,2],col="red")
> legend("topright",pch=c(15,15,1,19),color=c("black","red","black","black"),c("Alpha helical bundle","Beta barrel core", "Rotation","Translation")
+ )
Error in legend("topright", pch = c(15, 15, 1, 19), color = c("black",  : 
  unused argument (color = c("black", "red", "black", "black"))
> legend("topright",pch=c(15,15,1,19),col=c("black","red","black","black"),c("Alpha helical bundle","Beta barrel core", "Rotation","Translation"))
> dev.off()
quartz 
     2 
> psplotfilename="Metric_bundle_rotation_translation.eps"
> postscript(psplotfilename, height=4, width=3.5,pointsize=10, horizontal=FALSE, onefile=FALSE, paper=special)
Error in postscript(psplotfilename, height = 4, width = 3.5, pointsize = 10,  : 
  object 'special' not found
> psplotfilename="Metric_bundle_rotation_translation.eps"
> postscript(psplotfilename, height=4, width=3.5,pointsize=10, horizontal=FALSE, onefile=FALSE, paper='special')
> plot(bundle_rot[,2],xaxt="n",xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red",cex=1.5,)
> axis(1,labels=c("1N55","1KKO","1E15","3CH0","3CWN"),cex=1)
Error in axis(1, labels = c("1N55", "1KKO", "1E15", "3CH0", "3CWN"), cex = 1) : 
  'labels' is supplied and not 'at'
> axis(1,labels=c("1N55","1KKO","1E15","3CH0","3CWN"),at=c(1:5))
> points(bundle_rot[,1],cex=1.5)
> points(bundle_trans[,1],cex=1.5)
> points(bundle_trans[,2],cex=1.5,col="red")
> legend("topright",pch=c(15,15,1,19),col=c("black","red","black","black"),c("Alpha helical bundle","Beta barrel core", "Rotation","Translation"))
> dev.off()
quartz 
     2 
> plot(bundle_rot[,2],xaxt="n",xlab="PDB ID.",ylab=expression(Omega[w]),ylim=c(45,250),col="red",cex=1.5,pch=18)