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1 #!/usr/bin/env Rscript
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2 args = commandArgs(trailingOnly=TRUE)
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3 if (length(args)!=3) {
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4 st_sentence=paste("This script requires exactly 3 arguments",length(args),"supplied\n")
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5 stop(sentence, call.=FALSE)
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6 }
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7
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8 bubbleplot<-function(MatData,VirData,palette,magn,main,space)
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9 {
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10 COL=ncol(MatData)
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11 ROW=nrow(MatData)
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12 Mcopy=rep(1:COL,ROW)
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13 Mfactor=rep(1:ROW,rep( COL,ROW ))
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14
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15 COLOR=rep(palette,rep(COL,ROW))
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16 CEX=(log10(t((MatData*100)+1)))*magn
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17
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18
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19 par(mar=c(8,4,4,0),fig=c(0,0.8,0,1))
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20 plot(Mcopy,Mfactor,cex=0.1,pch=20,xaxt="n",yaxt="n",xlab="",ylab="",main=main,yaxs="r");
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21 #grid(COL*ROW)
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22 abline(h=1:ROW)
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23 abline(v=1:COL)
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24 lines(Mcopy,Mfactor,cex=CEX,col=COLOR,pch=20,type="p")
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25
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26 axis(1,at=1:COL,labels=colnames(MatData),las=2)
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27 axis(2,at=(1:ROW),labels=rownames(MatData),las=2)
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28
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29 par(fig=c(0.8,1,0,1),new=TRUE,mar=c(8,0,4,1))
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30 barplot(log10(VirData+1),horiz=T,las=2,space=space,yaxs="i",main="Log(N genomes)")
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31 }
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32 MatData=read.table("MatData.csv",header=T,row.names=1,check.names=F);
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33 VirData=read.table("VirData.csv",header=T,row.names=1);
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34 VirData=as.vector(VirData[,1])
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35 add_data=read.table(args[1],header=T,row.names=1,check.names=F);
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36 VirData=c(VirData,rep(1,nrow(add_data) ))
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37 MatData=rbind(MatData,add_data);
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38 pdf(args[2],width=1200,height=1600)
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39 bubbleplot(MatData,VirData,c(colors()[c(90,60,150,120,30)],topo.colors(nrow(add_data))),3,main="",space=1)
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40 dev.off()
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41 pdf(args[3],width=1600,height=1600)
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42 heatmap(cor(t(MatData)),col=blues9);
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43 dev.off()
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