| 1 |
|
| 2 |
DECOYSETS<-c("4state_reduced", "fisa", "fisa_casp3", "hg_structal", "ig_structal", "ig_structal_hires", "lattice_ssfit", "lmds", "vhp_mcmd","means") |
| 3 |
TYPES<-c("atomtype","atomcount","atomcomb","restype","rescount","rescomb") |
| 4 |
COLORS<-c(2,5,3,6,4,8) |
| 5 |
|
| 6 |
postscript("plots-means.ps") |
| 7 |
|
| 8 |
for (decoySet in DECOYSETS) { |
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data<-read.table(paste(decoySet,".summary",sep=""),header=FALSE) |
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data<-data[order(data$V3),] # sorting by cutoff ascending |
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|
| 12 |
# zscores |
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xlim<-c(min(data$V3),max(data$V3)) |
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#ylim<-c(min(data$V7),max(data$V7)) |
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ylim<-c(-2,6.5) |
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yspacing<-(ylim[2]-ylim[1])/25 |
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i=1 |
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for (type in TYPES) { |
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if (i==1) { |
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plot(data$V3[data$V2==type],data$V7[data$V2==type],xlim=xlim,ylim=ylim, |
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xlab="cutoff",ylab="zscore",main=paste("Mean native z-scores for decoy set '",decoySet,"' (size ",data$V5[1],")",sep=""), |
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type="b",col=COLORS[i]) |
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} else { |
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points(data$V3[data$V2==type],data$V7[data$V2==type],xlim=xlim,ylim=ylim,type="b",col=COLORS[i]) |
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} |
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legend(x=xlim[2]-3,y=ylim[2]-yspacing*i, type, col=COLORS[i], lty=1 , bty="n", pch=1) |
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i=i+1 |
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|
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} |
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abline(v=6,col=8,lty=2) |
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abline(h=seq(-2,6,2),col=8) |
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|
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# proportion native ranked 1 |
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ylim<-c(0,1) |
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yspacing<-(ylim[2]-ylim[1])/25 |
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i=1 |
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for (type in TYPES) { |
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if (i==1) { |
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plot(data$V3[data$V2==type],data$V6[data$V2==type],xlim=xlim,ylim=ylim, |
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xlab="cutoff",ylab="native ranked 1st",main=paste("Proportion of ranked-1st natives for decoy set '",decoySet,"' (size ",data$V5[1],")",sep=""), |
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type="b",col=COLORS[i]) |
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} else { |
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points(data$V3[data$V2==type],data$V6[data$V2==type],xlim=xlim,ylim=ylim,type="b",col=COLORS[i]) |
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} |
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legend(x=xlim[2]-3,y=ylim[2]-yspacing*i, type, col=COLORS[i], lty=1 , bty="n", pch=1) |
| 46 |
i=i+1 |
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|
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} |
| 49 |
abline(v=6,col=8,lty=2) |
| 50 |
|
| 51 |
# rank correlation |
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ylim<-c(0,1) |
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yspacing<-(ylim[2]-ylim[1])/25 |
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i=1 |
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for (type in TYPES) { |
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if (i==1) { |
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plot(data$V3[data$V2==type],-data$V8[data$V2==type],xlim=xlim,ylim=ylim, |
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xlab="cutoff",ylab="spearman",main=paste("Mean rank correlation for decoy set '",decoySet,"' (size ",data$V5[1],")",sep=""), |
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type="b",col=COLORS[i]) |
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} else { |
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points(data$V3[data$V2==type],-data$V8[data$V2==type],xlim=xlim,ylim=ylim,type="b",col=COLORS[i]) |
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} |
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legend(x=xlim[2]-3,y=ylim[2]-yspacing*i, type, col=COLORS[i], lty=1 , bty="n", pch=1) |
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i=i+1 |
| 65 |
|
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} |
| 67 |
abline(v=6,col=8,lty=2) |
| 68 |
|
| 69 |
} |
| 70 |
|
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dev.off() |
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|
| 73 |
|
| 74 |
DECOYSETS<-c("4state_reduced", "fisa", "fisa_casp3", "hg_structal", "ig_structal", "ig_structal_hires", "lattice_ssfit", "lmds", "vhp_mcmd") |
| 75 |
TYPES<-c("atomcomb","atomcount","atomtype","rescomb","rescount","restype") |
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COLORS<-c(2,2,2,4,4,4) |
| 77 |
PCHS<-c(1,4,5,1,4,5) |
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|
| 79 |
postscript("plots-individual.ps") |
| 80 |
all.atType.scores<-c() |
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all.atCount.scores<-c() |
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all.resType.scores<-c() |
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all.resCount.scores<-c() |
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|
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for (decoySet in DECOYSETS) { |
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data<-read.table(paste(decoySet,".indiv.summary",sep=""),header=FALSE) |
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# zscores |
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xlim<-c(1,dim(data)[1]) |
| 89 |
#ylim<-c(min(data$V6),max(data$V6)) |
| 90 |
ylim<-c(-2,6.5) |
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yspacing<-(ylim[2]-ylim[1])/25 |
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i=1 |
| 93 |
for (type in TYPES) { |
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if (i==1) { |
| 95 |
plot(data[,3*i],ylim=ylim, |
| 96 |
xlab="decoys",ylab="zscore",main=paste("z-scores for decoy set '",decoySet,"'",sep=""), |
| 97 |
type="p",pch=PCHS[i],col=COLORS[i], |
| 98 |
axes=FALSE) |
| 99 |
axis(2) |
| 100 |
axis(1, at=c(1:dim(data)[1]), labels=data$V1) |
| 101 |
box() |
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} else { |
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points(data[,3*i],ylim=ylim,type="p",pch=PCHS[i],col=COLORS[i]) |
| 104 |
} |
| 105 |
legend(x=xlim[2]-(xlim[2]-xlim[1])/10,y=ylim[2]-yspacing*(i-1), type, col=COLORS[i], lty=0 , bty="n", pch=PCHS[i]) |
| 106 |
i=i+1 |
| 107 |
|
| 108 |
} |
| 109 |
|
| 110 |
abline(v=c(1:dim(data)[1]),col=8,lty=3) |
| 111 |
|
| 112 |
all.atCount.scores<-c(all.atCount.scores,data$V3) |
| 113 |
all.atType.scores<-c(all.atType.scores,data$V6) |
| 114 |
all.resCount.scores<-c(all.resCount.scores,data$V9) |
| 115 |
all.resType.scores<-c(all.resType.scores,data$V12) |
| 116 |
|
| 117 |
|
| 118 |
} |
| 119 |
|
| 120 |
# correlation of z-scores atom type vs atom count |
| 121 |
corr<-cor(all.atCount.scores,all.atType.scores,method="spearman") |
| 122 |
plot(all.atCount.scores,all.atType.scores,xlab="z-score atom count",ylab="z-score atom type", |
| 123 |
main="correlation of z-scores atom type vs count") |
| 124 |
legend(x=max(all.atCount.scores)-2,y=min(all.atType.scores)+1,corr,col=3,bty="n") |
| 125 |
# correlation of z-scores res type vs res count |
| 126 |
corr<-cor(all.resCount.scores,all.resType.scores,method="spearman") |
| 127 |
plot(all.resCount.scores,all.resType.scores,xlab="z-score res count",ylab="z-score res type", |
| 128 |
main="correlation of z-scores res type vs count") |
| 129 |
legend(x=max(all.resCount.scores)-2,y=min(all.resType.scores)+1,corr,col=2,bty="n") |
| 130 |
dev.off() |
