Roopashree Shrivastava
2012-Jan-30 12:09 UTC
[R] about changing line type and line width in Taylor Diagram
Dear all,
I am new to plotting Taylor Diagram using plotrix package within R, hence
this post. I have written a script which plots Taylor Diagram with one
reference and 7 model values. However the font size, line width and line
type are not clear when saving the diagram as a jpeg file. I tried the
functions lty, lwd and font but no apparent change. I am attaching the
script here. Any help would be greatly appreciated. The script is
# my first taylor diagram
ref<-c(0.00640091,0.00533091,0.00381636,0.00275519,0.00277649,0.00280806,0.00267945,0.00237123,0.000970663,0.000986191,0.00100226,0.00086391,0.000622819,0.000485319,0.000362976,0.000246112,0.000165615,0.00008184,0.00004)
m1<-c(0.0124827,0.011662,0.0102956,0.0091183,0.00813907,0.007192,0.00662517,0.00433745,0.00184044,0.000649477,0.00024642,5.43E-05,0.000097696,0.000194817,0.000182709,0.000134398,0.000106024,8.92E-05,6.28E-05)
taylor.diagram(ref,m1,pos.cor=FALSE,ngamma=3,pcex=1,grad.corr.lines=c(-0.99,-0.95,-0.9,-0.8,-0.6,-0.4,-0.2,0,0.2,0.4,0.6,0.8,0.9,0.95,0.99),lty=1,lwd=10,font=5)
m2<-c(0.0101348,0.00920886,0.0086196,0.00785134,0.00723838,0.00675833,0.00579093,0.00540478,0.00226489,0.000809049,0.00019625,3.95E-05,8.89E-05,0.000195028,0.000185004,0.000131202,0.000109852,9.98E-05,6.80E-05)
taylor.diagram(ref,m2,add=TRUE,pch=19,col="blue",lty="solid",lwd=3)
m3<-c(0.0123251,0.0120384,0.00871793,0.00678519,0.00628331,0.00532673,0.00486861,0.0048328,0.0038655,0.00143683,0.00022057,8.61E-06,7.79E-05,0.000184976,0.000185927,0.000133771,0.000104613,9.26E-05,6.38E-05)
taylor.diagram(ref,m3,add=TRUE,pch=19,col="orange",lty="solid",lwd=3)
m4<-c(0.0134251,0.0126776,0.012559,0.0121933,0.0099911,0.00727952,0.00475407,0.00227909,0.00130748,0.000705607,0.000304828,5.70E-05,0.000109972,0.000187504,0.0002016,0.000133706,0.000109697,9.54E-05,6.35E-05)
taylor.diagram(ref,m4,add=TRUE,pch=19,col="pink",lty="solid",lwd=3)
m5<-c(0.0124275,0.0112242,0.00886243,0.00793019,0.0067846,0.00603205,0.00566561,0.00530552,0.00318331,0.000961854,0.000218234,3.66E-05,7.99E-05,0.000182724,0.000196627,0.000136862,0.000104907,0.000094622,6.20E-05)
taylor.diagram(ref,m5,add=TRUE,pch=19,col="purple",lty="solid",lwd=3)
m6<-c(0.0142817,0.0134474,0.0129694,0.0113914,0.0102208,0.00920309,0.00555206,0.00289796,0.00143831,0.000706277,0.000277201,5.60E-05,0.000114714,0.000186412,0.000198743,0.000134991,0.000108689,9.43E-05,6.16E-05)
taylor.diagram(ref,m6,add=TRUE,pch=19,col="brown",lty="solid",lwd=3)
m7<-c(0.0120621,0.0117936,0.00854782,0.00734006,0.00669576,0.00629334,0.00595018,0.00564455,0.00396859,0.000991006,0.000171742,9.68E-06,8.10E-05,0.000186982,0.00018854,0.000136548,0.000104581,9.18E-05,6.20E-05)
taylor.diagram(ref,m7,add=TRUE,pch=19,col="cyan",lty="solid",lwd=3)
lpos<-3.5*sd(ref)
legend(.75*lpos,1.5*lpos,legend=c("1111","1171","1211","2121","2221","4141","5251"),pch=19,col=c("red","blue","orange","pink","purple","brown","cyan"))
Thanking you,
Warm Regards
Roopa
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Jim Lemon
2012-Jan-31 08:20 UTC
[R] about changing line type and line width in Taylor Diagram
On 01/30/2012 11:09 PM, Roopashree Shrivastava wrote:> Dear all, > I am new to plotting Taylor Diagram using plotrix package within R, hence > this post. I have written a script which plots Taylor Diagram with one > reference and 7 model values. However the font size, line width and line > type are not clear when saving the diagram as a jpeg file. I tried the > functions lty, lwd and font but no apparent change. I am attaching the > script here. Any help would be greatly appreciated. The script is... >Hi Roopa, If by "not clear" you mean that the figure (especially the text) is generally a bit fuzzy, you probably want to use a device like PDF or Postscript. If you mean that you want larger text on the axes, I have added an argument "cex.axis" to the function below that allows the user to get a bit of text expansion. This will appear in the next version of plotrix. About line width and type, there seems to be a convention on the line types used in Taylor diagrams, but additional arguments could be added to modify these if you really need them. If you want to change the font, do it as in the example below. I found that using only the positive correlations produced a much clearer plot, so you may want to try this somewhat altered example: ref<-c(0.00640091,0.00533091,0.00381636,0.00275519,0.00277649, 0.00280806,0.00267945,0.00237123,0.000970663,0.000986191, 0.00100226,0.00086391,0.000622819,0.000485319, 0.000362976,0.000246112,0.000165615,0.00008184,0.00004) m1<-c(0.0124827,0.011662,0.0102956,0.0091183,0.00813907, 0.007192,0.00662517,0.00433745,0.00184044,0.000649477, 0.00024642,5.43E-05,0.000097696,0.000194817, 0.000182709,0.000134398,0.000106024,8.92E-05,6.28E-05) m2<-c(0.0101348,0.00920886,0.0086196,0.00785134,0.00723838, 0.00675833,0.00579093,0.00540478,0.00226489,0.000809049, 0.00019625,3.95E-05,8.89E-05,0.000195028, 0.000185004,0.000131202,0.000109852,9.98E-05,6.80E-05) m3<-c(0.0123251,0.0120384,0.00871793,0.00678519,0.00628331, 0.00532673,0.00486861,0.0048328,0.0038655,0.00143683, 0.00022057,8.61E-06,7.79E-05,0.000184976, 0.000185927,0.000133771,0.000104613,9.26E-05,6.38E-05) m4<-c(0.0134251,0.0126776,0.012559,0.0121933,0.0099911, 0.00727952,0.00475407,0.00227909,0.00130748,0.000705607, 0.000304828,5.70E-05,0.000109972,0.000187504, 0.0002016,0.000133706,0.000109697,9.54E-05,6.35E-05) m5<-c(0.0124275,0.0112242,0.00886243,0.00793019,0.0067846, 0.00603205,0.00566561,0.00530552,0.00318331,0.000961854, 0.000218234,3.66E-05,7.99E-05,0.000182724, 0.000196627,0.000136862,0.000104907,0.000094622,6.20E-05) m6<-c(0.0142817,0.0134474,0.0129694,0.0113914,0.0102208, 0.00920309,0.00555206,0.00289796,0.00143831,0.000706277, 0.000277201,5.60E-05,0.000114714,0.000186412, 0.000198743,0.000134991,0.000108689,9.43E-05,6.16E-05) m7<-c(0.0120621,0.0117936,0.00854782,0.00734006,0.00669576, 0.00629334,0.00595018,0.00564455,0.00396859,0.000991006, 0.000171742,9.68E-06,8.10E-05,0.000186982, 0.00018854,0.000136548,0.000104581,9.18E-05,6.20E-05) par(family="serif") taylor.diagram(ref,m1,ngamma=3,pch=19,pcex=2,cex.axis=1.2, lty=1,lwd=10,font=5) taylor.diagram(ref,m2,add=TRUE,pch=19,pcex=2,col="blue", lty="solid",lwd=3) taylor.diagram(ref,m3,add=TRUE,pch=19,pcex=2,col="orange", lty="solid",lwd=3) taylor.diagram(ref,m4,add=TRUE,pch=19,pcex=2,col="pink", lty="solid",lwd=3) taylor.diagram(ref,m5,add=TRUE,pch=19,pcex=2,col="purple", lty="solid",lwd=3) taylor.diagram(ref,m6,add=TRUE,pch=19,pcex=2,col="brown", lty="solid",lwd=3) taylor.diagram(ref,m7,add=TRUE,pch=19,pcex=2,col="cyan", lty="solid",lwd=3) lpos<-3.5*sd(ref) legend(lpos,1.1*lpos, legend=c("1111","1171","1211","2121","2221","4141","5251"), pch=19, col=c("red","blue","orange","pink","purple","brown","cyan")) Jim # Display a Taylor diagram # Taylor K.E. (2001) # Summarizing multiple aspects of model performance in a single diagram # Journal of Geophysical Research, 106: 7183-7192. # version 1.0 # progr. Olivier.Eterradossi, 12/2007 # 2007-01-12 - modifications and Anglicizing - Jim Lemon # version 2.0 # progr. initiale OLE, 8/01/2007 # rev. OLE 3/09/2008 : remove samples with NA's from mean, sd and cor calculations # 2008-09-04 - integration and more anglicizing - Jim Lemon # 2008-12-09 - added correlation radii, sd arcs to the pos.cor=FALSE routine # and stopped the pos.cor=FALSE routine from calculating arcs for zero radius # Jim Lemon # 2010-4-30 - added the gamma.col argument for pos.cor=TRUE plots - Jim Lemon # 2010-6-24 - added mar argument to pos.cor=TRUE plots - Jim Lemon # 2012-1-31 - added the cex.axis argument - Jim Lemon taylor.diagram<-function(ref,model,add=FALSE,col="red",pch=19,pos.cor=TRUE, xlab="",ylab="",main="Taylor Diagram",show.gamma=TRUE,ngamma=3,gamma.col=8, sd.arcs=0,ref.sd=FALSE,grad.corr.lines=c(0.2,0.4,0.6,0.8,0.9),pcex=1, cex.axis=1,normalize=FALSE,mar=c(5,4,6,6),...) { grad.corr.full<-c(0,0.2,0.4,0.6,0.8,0.9,0.95,0.99,1) R<-cor(ref,model,use="pairwise") sd.r<-sd(ref) sd.f<-sd(model) if(normalize) { sd.f<-sd.f/sd.r sd.r<-1 } maxsd<-1.5*max(sd.f,sd.r) oldpar<-par("mar","xpd","xaxs","yaxs") if(!add) { # display the diagram if(pos.cor) { if(nchar(ylab) == 0) ylab="Standard deviation" par(mar=mar) plot(0,xlim=c(0,maxsd),ylim=c(0,maxsd),xaxs="i",yaxs="i",axes=FALSE, main=main,xlab=xlab,ylab=ylab,type="n",cex=cex.axis,...) if(grad.corr.lines[1]) { for(gcl in grad.corr.lines) lines(c(0,maxsd*gcl),c(0,maxsd*sqrt(1-gcl^2)),lty=3) } # add the axes segments(c(0,0),c(0,0),c(0,maxsd),c(maxsd,0)) axis.ticks<-pretty(c(0,maxsd)) axis.ticks<-axis.ticks[axis.ticks<=maxsd] axis(1,at=axis.ticks,cex.axis=cex.axis) axis(2,at=axis.ticks,cex.axis=cex.axis) if(sd.arcs[1]) { if(length(sd.arcs) == 1) sd.arcs<-axis.ticks for(sdarc in sd.arcs) { xcurve<-cos(seq(0,pi/2,by=0.03))*sdarc ycurve<-sin(seq(0,pi/2,by=0.03))*sdarc lines(xcurve,ycurve,col="blue",lty=3) } } if(show.gamma[1]) { # if the user has passed a set of gamma values, use that if(length(show.gamma) > 1) gamma<-show.gamma # otherwise make up a set else gamma<-pretty(c(0,maxsd),n=ngamma)[-1] if(gamma[length(gamma)] > maxsd) gamma<-gamma[-length(gamma)] labelpos<-seq(45,70,length.out=length(gamma)) # do the gamma curves for(gindex in 1:length(gamma)) { xcurve<-cos(seq(0,pi,by=0.03))*gamma[gindex]+sd.r # find where to clip the curves endcurve<-which(xcurve<0) endcurve<-ifelse(length(endcurve),min(endcurve)-1,105) ycurve<-sin(seq(0,pi,by=0.03))*gamma[gindex] maxcurve<-xcurve*xcurve+ycurve*ycurve startcurve<-which(maxcurve>maxsd*maxsd) startcurve<-ifelse(length(startcurve),max(startcurve)+1,0) lines(xcurve[startcurve:endcurve],ycurve[startcurve:endcurve], col=gamma.col) if(xcurve[labelpos[gindex]] > 0) boxed.labels(xcurve[labelpos[gindex]],ycurve[labelpos[gindex]], gamma[gindex],border=FALSE) } } # the outer curve for correlation xcurve<-cos(seq(0,pi/2,by=0.01))*maxsd ycurve<-sin(seq(0,pi/2,by=0.01))*maxsd lines(xcurve,ycurve) bigtickangles<-acos(seq(0.1,0.9,by=0.1)) medtickangles<-acos(seq(0.05,0.95,by=0.1)) smltickangles<-acos(seq(0.91,0.99,by=0.01)) segments(cos(bigtickangles)*maxsd,sin(bigtickangles)*maxsd, cos(bigtickangles)*0.97*maxsd,sin(bigtickangles)*0.97*maxsd) par(xpd=TRUE) if(ref.sd) { # the inner curve for reference SD xcurve<-cos(seq(0,pi/2,by=0.01))*sd.r ycurve<-sin(seq(0,pi/2,by=0.01))*sd.r lines(xcurve,ycurve) } points(sd.r,0,cex=pcex) text(cos(c(bigtickangles,acos(c(0.95,0.99))))*1.05*maxsd, sin(c(bigtickangles,acos(c(0.95,0.99))))*1.05*maxsd, c(seq(0.1,0.9,by=0.1),0.95,0.99)) text(maxsd*0.8,maxsd*0.8,"Correlation",srt=315) segments(cos(medtickangles)*maxsd,sin(medtickangles)*maxsd, cos(medtickangles)*0.98*maxsd,sin(medtickangles)*0.98*maxsd) segments(cos(smltickangles)*maxsd,sin(smltickangles)*maxsd, cos(smltickangles)*0.99*maxsd,sin(smltickangles)*0.99*maxsd) } else { x<- ref y<- model R<-cor(x,y,use="pairwise.complete.obs") E<-mean(x,na.rm=TRUE)-mean(y,na.rm=TRUE) # overall bias xprime<-x-mean(x,na.rm=TRUE) yprime<-y-mean(y,na.rm=TRUE) sumofsquares<-(xprime-yprime)^2 Eprime<-sqrt(sum(sumofsquares)/length(complete.cases(x))) # centered pattern RMS E2<-E^2+Eprime^2 if (add==FALSE) { # pourtour du diagramme (display the diagram) maxray<-1.5*max(sd.f,sd.r) plot(c(-maxray,maxray),c(0,maxray),type="n",asp=1,bty="n",xaxt="n",yaxt="n", xlab=xlab,ylab=ylab,main=main,cex=cex.axis) discrete<-seq(180,0,by=-1) listepoints<-NULL for (i in discrete){ listepoints<-cbind(listepoints,maxray*cos(i*pi/180),maxray*sin(i*pi/180)) } listepoints<-matrix(listepoints,2,length(listepoints)/2) listepoints<-t(listepoints) lines(listepoints[,1],listepoints[,2]) # axes x,y lines(c(-maxray,maxray),c(0,0)) lines(c(0,0),c(0,maxray)) # lignes radiales jusqu'? R = +/- 0.8 for (i in grad.corr.lines){ lines(c(0,maxray*i),c(0,maxray*sqrt(1-i^2)),lty=3) lines(c(0,-maxray*i),c(0,maxray*sqrt(1-i^2)),lty=3) } # texte radial for (i in grad.corr.full){ text(1.05*maxray*i,1.05*maxray*sqrt(1-i^2),i,cex=0.6) text(-1.05*maxray*i,1.05*maxray*sqrt(1-i^2),-i,cex=0.6) } # sd concentriques autour de la reference seq.sd<-seq.int(0,2*maxray,by=(maxray/10))[-1] for (i in seq.sd){ xcircle<-sd.r+(cos(discrete*pi/180)*i) ycircle<-sin(discrete*pi/180)*i for (j in 1:length(xcircle)){ if ((xcircle[j]^2+ycircle[j]^2)<(maxray^2)){ points(xcircle[j],ycircle[j], col="darkgreen",pch=".") if(j==10) text(xcircle[j],ycircle[j],signif(i,2),cex=0.5,col="darkgreen") } } } # sd concentriques autour de l'origine seq.sd<-seq.int(0,maxray,length.out=5) for (i in seq.sd){ xcircle<-(cos(discrete*pi/180)*i) ycircle<-sin(discrete*pi/180)*i if(i) lines(xcircle,ycircle,lty=3,col="blue") text(min(xcircle),-0.03*maxray,signif(i,2),cex=0.5,col="blue") text(max(xcircle),-0.03*maxray,signif(i,2),cex=0.5,col="blue") } text(0,-0.08*maxray,"Standard Deviation",cex=0.7,col="blue") text(0,-0.12*maxray,"Centered RMS Difference",cex=0.7,col="darkgreen") points(sd.r,0,pch=22,bg="darkgreen",cex=1.1) text(0,1.1*maxray,"Correlation Coefficient",cex=0.7) } S<-(2*(1+R))/(sd.f+(1/sd.f))^2 # Taylor<-S } } # display the points points(sd.f*R,sd.f*sin(acos(R)),pch=pch,col=col,cex=pcex) invisible(oldpar) }