R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0] [Workspace restored from /Users/sandhyatiwari/.RData] [History restored from /Users/sandhyatiwari/.Rapp.history] > does this work? Error: unexpected symbol in "does this" > maybe Error: object 'maybe' not found > plot(x=y) Error in plot(x = y) : object 'y' not found > x=10 > plot(x=y) Error in plot(x = y) : object 'y' not found > plot(x) > fluct<-read.table(file.choose(),na.strings=c("NaN") + ) > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 0.02604167 0.03875969 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] 0 1 0 1 $xaxp [1] 0 1 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 1 5 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,15),col=color_profile[1]) Error in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, : formal argument "lty" matched by multiple actual arguments In addition: Warning message: In plot.window(xlim, ylim, log = log, ...) : graphical parameter "type" is obsolete > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > color_profile = rainbow(dim(fluct)[2]) > layout(matrix(1,2,nrow=2,ncol=1),heights=(4,1)) Error: unexpected ',' in "layout(matrix(1,2,nrow=2,ncol=1),heights=(4," > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 0.02604167 0.03875969 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] 0 1 0 1 $xaxp [1] 0 1 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 1 5 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,15),col=color_profile[1]) Error in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, : formal argument "lty" matched by multiple actual arguments In addition: Warning message: In plot.window(xlim, ylim, log = log, ...) : graphical parameter "type" is obsolete > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,15),col=color_profile[1]) Error in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, : formal argument "lty" matched by multiple actual arguments In addition: Warning message: In plot.window(xlim, ylim, log = log, ...) : graphical parameter "type" is obsolete > plot(fluct[,1], lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,15),col=color_profile[1]) Error in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, : formal argument "lty" matched by multiple actual arguments > ?(plot) starting httpd help server ... done > plot function (x, y, ...) UseMethod("plot") > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,15),col=color_profile[1]) Error in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, : formal argument "lty" matched by multiple actual arguments In addition: Warning message: In plot.window(xlim, ylim, log = log, ...) : graphical parameter "type" is obsolete > plot(fluct) > plot(fluct[,1]) > fluct<-read.table(file.choose(),header=TRUE) > plot(fluct[,1]) > plot(fluct[,1],type="l",lty="dotted",xlab="alignment index") > plot(fluct[,1],type="l",lty="dotted",xlab="alignment index") > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,15),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) Error: unexpected '>' in ">" > > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) Error: unexpected '>' in ">" > > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) Error: unexpected '>' in ">" > > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) Error: unexpected '>' in ">" > > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) Error: unexpected '>' in ">" > > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) Error: unexpected '>' in ">" > points(fluct[,2],type="l",lty="dotted",col=color_profile[2])points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) Error: unexpected symbol in "points(fluct[,2],type="l",lty="dotted",col=color_profile[2])points" > > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) Error: unexpected '>' in ">" > > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) Error: unexpected '>' in ">" > > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) Error: unexpected '>' in ">" > > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) Error: unexpected '>' in ">" > > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) Error: unexpected '>' in ">" > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 6.946875 0.627907 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] -8.88 257.88 -0.60 15.60 $xaxp [1] 0 250 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 15 3 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,15),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > legend("topright", c("",""), col=c("orange","blue"),lwd=1,lty=c(0,0),box.lwd=0) > legend("topright", c("",""), col=c("orange","blue"),lwd=1,lty=c(0,0),box.lwd=0) > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 0.02604167 0.03875969 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] 0 1 0 1 $xaxp [1] 0 1 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 1 5 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,15),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 6.946875 0.627907 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] -8.88 257.88 -0.60 15.60 $xaxp [1] 0 250 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 15 3 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,10),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 6.9468750 0.4186047 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] -8.88 257.88 -0.40 10.40 $xaxp [1] 0 250 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 10 5 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,8),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > headers(fluct) Error: could not find function "headers" > header(fluct) Error: could not find function "header" > summary(fluct) X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1ak2.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1ake.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1aky.mode.A. Min. :0.02836 Min. :0.08466 Min. :0.07451 1st Qu.:0.08613 1st Qu.:0.18074 1st Qu.:0.17458 Median :0.14628 Median :0.27557 Median :0.26397 Mean :0.45454 Mean :0.46729 Mean :0.45872 3rd Qu.:0.36352 3rd Qu.:0.54823 3rd Qu.:0.50368 Max. :4.75711 Max. :3.67991 Max. :5.39677 NA's :28 NA's :34 NA's :30 X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1dvr.mode.B. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.2ak3.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.2aky.mode.A. Min. :0.03828 Min. : 0.00309 Min. :0.08067 1st Qu.:0.10368 1st Qu.: 0.01123 1st Qu.:0.18552 Median :0.18531 Median : 0.02269 Median :0.28358 Mean :0.45454 Mean : 0.44248 Mean :0.45872 3rd Qu.:0.40578 3rd Qu.: 0.06762 3rd Qu.:0.52434 Max. :6.73664 Max. :45.18387 Max. :3.88312 NA's :28 NA's :22 NA's :30 X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.2eck.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.4ake.mode.A. Min. :0.07676 Min. :0.01535 1st Qu.:0.18757 1st Qu.:0.06193 Median :0.28414 Median :0.11989 Mean :0.46729 Mean :0.46729 3rd Qu.:0.58215 3rd Qu.:0.30981 Max. :3.63095 Max. :6.72472 NA's :34 NA's :34 > summary(fluct) X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1ak2.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1ake.mode.A. Min. :0.02836 Min. :0.08466 1st Qu.:0.08613 1st Qu.:0.18074 Median :0.14628 Median :0.27557 Mean :0.45454 Mean :0.46729 3rd Qu.:0.36352 3rd Qu.:0.54823 Max. :4.75711 Max. :3.67991 NA's :28 NA's :34 X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1aky.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1dvr.mode.B. Min. :0.07451 Min. :0.03828 1st Qu.:0.17458 1st Qu.:0.10368 Median :0.26397 Median :0.18531 Mean :0.45872 Mean :0.45454 3rd Qu.:0.50368 3rd Qu.:0.40578 Max. :5.39677 Max. :6.73664 NA's :30 NA's :28 X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.2ak3.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.2aky.mode.A. Min. : 0.00309 Min. :0.08067 1st Qu.: 0.01123 1st Qu.:0.18552 Median : 0.02269 Median :0.28358 Mean : 0.44248 Mean :0.45872 3rd Qu.: 0.06762 3rd Qu.:0.52434 Max. :45.18387 Max. :3.88312 NA's :22 NA's :30 X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.2eck.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.4ake.mode.A. Min. :0.07676 Min. :0.01535 1st Qu.:0.18757 1st Qu.:0.06193 Median :0.28414 Median :0.11989 Mean :0.46729 Mean :0.46729 3rd Qu.:0.58215 3rd Qu.:0.30981 Max. :3.63095 Max. :6.72472 NA's :34 NA's :34 > names<-c("1AK2 A","1AKE A","1AKY A","1DVR B","2AK3 A","2AKY A","2ECK A","4AKE A") > legend("topleft",names,fill=colour_profile[1:8]) Error in legend("topleft", names, fill = colour_profile[1:8]) : object 'colour_profile' not found > legend("topleft",names,fill=color_profile[1:8]) > LID<-c(0, 132:179) > LID [1] 0 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 > LID<-c(132:179) > LD Error: object 'LD' not found > LID [1] 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 > LID<-c(132:179,0) > LID [1] 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 0 > LID<-seq(0,132:179) Error in seq.default(0, 132:179) : 'to' must be of length 1 > LID<-seq(132:179,0) Error in seq.default(132:179, 0) : 'from' must be of length 1 > LID<-matrix(132:179,0) Error in matrix(132:179, 0) : data is too long > LID<-array(132:179,0) > LID integer(0) > LID<-array(0,dim=132:179) Error in array(0, dim = 132:179) : negative length vectors are not allowed > LID<-array(0,dim=length(132:179)) > LID [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LID<-seq(132:179) > LID [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 > LID<-c(132:179) > LID [1] 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 > NMP<-c(38:75) > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 6.9468750 0.3348837 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] -8.88 257.88 -0.32 8.32 $xaxp [1] 0 250 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 8 4 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,8),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > points(fluct[,1],type="l",col=color_profile[1]) > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 0.02604167 0.03875969 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] 0 1 0 1 $xaxp [1] 0 1 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 1 5 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,8),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > points(NMP,array(0,dim=length(NMP),pch=20,col="gray") + ) Error in array(0, dim = length(NMP), pch = 20, col = "gray") : unused arguments (pch = 20, col = "gray") > points(NMP,array(0,dim=length(NMP)),pch=20,col="gray") > points(NMP,array(-0.1,dim=length(NMP)),pch=20,col="gray") > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 6.9468750 0.3348837 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] -8.88 257.88 -0.32 8.32 $xaxp [1] 0 250 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 8 4 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,8),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > points(NMP,array(-0.1,dim=length(NMP)),pch=20,col="gray") > points(LID,array(-0.1,dim=length(LID)),pch=20,col="black") > conserved_fluct<-read.table(file.choose(),header=TRUE) > conserved_fluct index X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1ak2.mode.A. X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1ake.mode.A. 1 0 NaN NaN 2 1 NaN NaN 3 2 NaN NaN 4 3 NaN NaN 5 4 NaN NaN 6 5 NaN NaN 7 6 NaN NaN 8 7 0.09430557 0.60033887 9 8 0.03776239 0.16338363 10 9 0.04647293 0.13496837 11 10 0.02918106 0.09318697 12 11 0.03651157 0.10228196 13 12 0.04112091 0.11486355 14 13 0.06445591 0.16661706 15 14 0.12308267 0.20659390 16 15 0.19352044 0.30391036 17 16 0.11506337 0.17686133 18 17 0.05713371 0.10916889 19 18 0.08403791 0.14671515 20 19 NaN NaN 21 20 0.07912100 0.14418759 22 21 0.11456408 0.14082910 23 22 0.11928246 0.13697134 24 23 0.08553285 0.13982074 25 24 0.07242816 0.21849986 26 25 0.11176422 0.26008340 27 26 0.13443089 0.21563859 28 27 0.08884255 0.18167444 29 28 0.06703078 0.52268981 30 29 0.16474535 0.74783851 31 30 0.20865587 0.67701874 32 31 0.14675026 0.51692577 33 32 0.12409153 0.26142392 34 33 NaN NaN 35 34 0.06087161 0.20826790 36 35 0.05328504 0.13438738 37 36 0.06543548 0.13934118 38 37 0.09202257 0.12462417 39 38 0.14114252 0.13619288 40 39 0.34698495 0.21890968 41 40 0.26307580 0.21702729 42 41 0.12861118 0.17403317 43 42 0.16762575 0.14202805 44 43 0.37968463 0.24679660 45 44 0.42372849 0.29001442 46 45 0.22928120 0.17729053 47 46 0.30116126 0.21235818 48 47 0.82587040 0.65079372 49 48 1.04121349 1.04510317 50 49 1.02125893 0.77628661 51 50 1.06223222 0.75948784 52 51 1.06088086 1.05961330 53 52 0.43916457 0.93689192 54 53 0.28013103 0.20416393 55 54 0.60476134 0.18925545 56 55 0.62104918 0.40904701 57 56 0.33162925 0.27858964 58 57 0.65472007 0.37747944 59 58 1.20908535 0.31113741 60 59 0.94898136 0.19403266 61 60 1.30033503 0.19075036 62 61 3.29438044 0.25754995 63 62 4.75710926 0.26348947 64 63 4.64443232 0.20441576 65 64 3.01758492 0.30881873 66 65 2.87214863 1.03647155 67 66 0.83911781 0.55499014 68 67 0.53590311 0.43722898 69 68 0.29974374 0.30723336 70 69 0.26513415 0.36622029 71 70 0.15845367 0.25238191 72 71 0.11381530 0.19203818 73 72 0.09698524 0.20792882 74 73 0.10269686 0.23773923 75 74 0.09100035 0.24325784 76 75 0.07813741 0.21707087 77 76 0.09684475 0.34143079 78 77 0.14185470 0.44468523 79 78 0.11690595 0.41485308 80 79 0.10862397 0.44986906 81 80 0.24513983 0.99353433 82 81 NaN NaN 83 82 0.27930163 1.33229648 84 83 NaN NaN 85 84 0.27533238 1.34862758 86 85 0.06359967 0.36274935 87 86 0.18423706 1.43275145 88 87 0.09264883 1.06662448 89 88 0.04297739 0.24807282 90 89 0.03813054 0.12806520 91 90 0.03048672 0.08465653 92 91 0.03259613 0.08635990 93 92 0.03913912 0.08506341 94 93 0.05506173 0.12170272 95 94 0.08328607 0.15872288 96 95 0.10255143 0.17482037 97 96 0.14580639 0.21181293 98 97 0.09467786 0.16280788 99 98 0.08954555 0.24450261 100 99 0.10791896 0.25134462 101 100 0.06145947 0.12627808 102 101 0.05390838 0.15308003 103 102 0.09021367 0.28076263 104 103 0.08526995 0.30474672 105 104 0.06829184 0.28088712 106 105 0.08715338 0.41834397 107 106 0.13219071 1.01389573 108 107 0.11068593 0.93936069 109 108 0.08377363 1.13546610 110 109 NaN NaN 111 110 NaN NaN 112 111 NaN NaN 113 112 NaN NaN 114 113 NaN NaN 115 114 0.22098049 0.94267680 116 115 0.06943765 0.31953091 117 116 0.04518389 0.16908620 118 117 0.03793138 0.13351018 119 118 0.02835840 0.10231090 120 119 0.03582047 0.11825624 121 120 0.03517817 0.10181014 122 121 0.04456269 0.10140414 123 122 0.06323716 0.18833831 124 123 0.11219763 0.26248195 125 124 0.19021108 0.67666088 126 125 NaN NaN 127 126 0.19393638 0.60069562 128 127 0.23658391 0.93439995 129 128 0.12218776 0.47856274 130 129 0.07041235 0.19975952 131 130 0.12011812 0.22965436 132 131 0.13919606 0.28790983 133 132 0.09335570 0.20342488 134 133 0.10929697 0.14167275 135 134 0.16585281 0.18922820 136 135 0.15696752 0.23615447 137 136 0.12431760 0.18043457 138 137 NaN NaN 139 138 0.25893256 0.16410777 140 139 0.46208132 0.16747964 141 140 1.61038048 0.41649552 142 141 NaN NaN 143 142 NaN NaN 144 143 3.43357089 0.97374791 145 144 2.76520049 0.74197984 146 145 1.57665290 0.37581966 147 146 0.73011796 0.26333869 148 147 0.23998347 0.25574504 149 148 0.12585981 0.20281545 150 149 0.08448977 0.15032335 151 150 NaN NaN 152 151 NaN NaN 153 152 0.17715546 0.81819359 154 153 0.15655550 0.46522508 155 154 0.23981354 0.35360120 156 155 0.48636411 0.68491436 157 156 1.74303068 2.49503260 158 157 1.65940621 2.17138036 159 158 1.04297432 1.52720886 160 159 0.57415565 0.91260642 161 160 0.56552747 0.51269639 162 161 0.61853163 0.44091263 163 162 1.56918009 1.48815763 164 163 3.75808597 3.67991225 165 164 3.65169901 3.03934964 166 165 NaN NaN 167 166 1.69011278 1.36911226 168 167 0.75954705 0.77918435 169 168 0.31225210 0.26172648 170 169 0.49096989 0.48928673 171 170 0.41713989 0.41142900 172 171 0.50234548 0.63376848 173 172 0.58977015 0.81626004 174 173 NaN NaN 175 174 NaN NaN 176 175 NaN NaN 177 176 NaN NaN 178 177 NaN NaN 179 178 1.39288798 0.37455364 180 179 0.57247005 0.28092683 181 180 1.11771281 0.24886928 182 181 1.08694241 0.13102466 183 182 0.35813084 0.12826019 184 183 0.29824541 0.16419274 185 184 0.42632767 0.12474630 186 185 0.34390178 0.10519757 187 186 0.16839323 0.12705197 188 187 0.25507412 0.19467764 189 188 0.26759245 0.16500086 190 189 0.15098654 0.12470333 191 190 0.15094210 0.23112314 192 191 0.19040571 0.30345707 193 192 0.15032571 0.22727497 194 193 0.08632531 0.11713509 195 194 0.14496287 0.21034606 196 195 0.11789824 0.26640884 197 196 0.05682094 0.18422386 198 197 0.07337581 0.25886325 199 198 0.11541001 0.35100174 200 199 0.08496691 0.27734331 201 200 0.04937128 0.21287901 202 201 0.07808754 0.27379590 203 202 0.21247637 0.45664958 204 203 0.18820674 0.31803527 205 204 0.15688495 0.20743149 206 205 NaN NaN 207 206 NaN NaN 208 207 NaN NaN 209 208 NaN NaN 210 209 NaN NaN 211 210 0.08282079 0.20806509 212 211 0.04754220 0.17691713 213 212 0.06334608 0.28628565 214 213 0.05866895 0.23090705 215 214 0.08116348 0.30195658 216 215 0.07746895 0.28533603 217 216 NaN NaN 218 217 0.12066951 0.57911059 219 218 0.11353010 0.47467730 220 219 0.14192240 0.67414314 221 220 0.16106570 0.58242022 222 221 0.21769179 0.70846108 223 222 0.13033625 0.42302709 224 223 0.07254014 0.25023794 225 224 0.09680811 0.31443832 226 225 0.12051579 0.43772492 227 226 0.09360160 0.44472500 228 227 0.07953490 0.36152814 229 228 0.10438729 0.52793913 230 229 0.11553751 0.81699727 231 230 0.09023279 0.95698535 232 231 0.07207312 1.28697632 233 232 0.14965914 3.08198186 234 233 NaN NaN 235 234 NaN NaN 236 235 NaN NaN 237 236 NaN NaN 238 237 NaN NaN 239 238 NaN NaN 240 239 NaN NaN 241 240 NaN NaN 242 241 NaN NaN 243 242 NaN NaN 244 243 NaN NaN 245 244 NaN NaN 246 245 NaN NaN 247 246 NaN NaN 248 247 NaN NaN X..Users.sandhyatiwari.local.webnma.api.webnma.api.parts.scratch.1aky.mode.A. 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0.58542854 0.09949272 128 0.85335431 0.13302756 129 0.41406106 0.08905282 130 0.18157301 0.05278516 131 0.22337612 0.06627974 132 0.27348133 0.09344546 133 0.19337686 0.08524104 134 0.13196188 0.06732655 135 0.16547116 0.06821180 136 0.22981440 0.08915373 137 0.17284967 0.09566231 138 NaN NaN 139 0.16652307 0.36781071 140 0.15531083 1.01015661 141 0.38746084 2.50233806 142 NaN NaN 143 NaN NaN 144 0.93337562 6.72471809 145 0.77375081 6.65500796 146 0.34737882 3.92558980 147 0.25293572 2.17213070 148 0.24502449 0.76921546 149 0.19871386 0.35586440 150 0.14786736 0.22209286 151 NaN NaN 152 NaN NaN 153 0.88329651 1.46743886 154 0.47987513 1.19602619 155 0.34616394 0.78237640 156 0.77697808 1.00917240 157 2.45416969 3.01324126 158 2.09565641 2.52996458 159 1.80147248 1.34952539 160 0.99155821 0.84161172 161 0.53743291 1.03387475 162 0.44177314 1.22665954 163 1.40542688 2.90441411 164 3.63095452 6.56918267 165 3.25485117 6.24337373 166 NaN NaN 167 1.39278450 2.91784970 168 0.86993795 1.38329872 169 0.29817225 0.48392273 170 0.43344993 0.45883081 171 0.37139491 0.29696296 172 0.61058664 0.56058166 173 0.80820301 0.77629563 174 NaN NaN 175 NaN NaN 176 NaN NaN 177 NaN NaN 178 NaN NaN 179 0.32394631 0.21995381 180 0.24762563 0.18150591 181 0.25813686 0.42279032 182 0.13961777 0.30403898 183 0.13022250 0.11999338 184 0.16954874 0.15072632 185 0.14379480 0.21030516 186 0.11167651 0.15322213 187 0.13763877 0.09436972 188 0.19149564 0.13776956 189 0.17754086 0.14651930 190 0.13047283 0.07995182 191 0.22876389 0.07683846 192 0.29919486 0.11774933 193 0.23655447 0.08451225 194 0.12203927 0.04395100 195 0.21080848 0.07372873 196 0.30587974 0.05548018 197 0.19063059 0.02633314 198 0.27218248 0.03797467 199 0.34338105 0.05496065 200 0.27243113 0.03892914 201 0.21404314 0.03000434 202 0.29012121 0.04816288 203 0.47624169 0.08727682 204 0.31643821 0.05519524 205 0.19113699 0.03911267 206 NaN NaN 207 NaN NaN 208 NaN NaN 209 NaN NaN 210 NaN NaN 211 0.19817601 0.03280834 212 0.19409057 0.02900718 213 0.26414191 0.05198803 214 0.21895890 0.04816102 215 0.33146847 0.05465616 216 0.29968855 0.07637317 217 NaN NaN 218 0.60665869 0.18421654 219 0.55629821 0.23672231 220 0.68975388 0.35554995 221 0.61567623 0.31173917 222 0.84969999 0.37797023 223 0.45820413 0.22851025 224 0.28723325 0.11550334 225 0.33955259 0.14000571 226 0.45181305 0.18901112 227 0.41624474 0.13359470 228 0.36060472 0.09430659 229 0.49341200 0.13835442 230 0.70574517 0.19030580 231 0.90287278 0.16094744 232 1.36384429 0.18980552 233 2.92142126 0.40371832 234 NaN NaN 235 NaN NaN 236 NaN NaN 237 NaN NaN 238 NaN NaN 239 NaN NaN 240 NaN NaN 241 NaN NaN 242 NaN NaN 243 NaN NaN 244 NaN NaN 245 NaN NaN 246 NaN NaN 247 NaN NaN 248 NaN NaN > > points(conserved_fluct[,1],type="l", col=color_profile[1]) > points(conserved_fluct[,2],type="l",col=color_profile[2]) > points(conserved_fluct[,3],type="l",col=color_profile[3]) > points(conserved_fluct[,4],type="l",col=color_profile[4]) > points(conserved_fluct[,5],type="l",col=color_profile[5]) > points(conserved_fluct[,6],type="l",col=color_profile[6]) > points(conserved_fluct[,7],type="l",col=color_profile[7]) > points(conserved_fluct[,8],type="l",col=color_profile[8]) > points(conserved_fluct[,1],type="l",col=color_profile[1]) > points(conserved_fluct[,2],type="l",col=color_profile[2]) > points(conserved_fluct[,3],type="l",col=color_profile[3]) > points(conserved_fluct[,4],type="l",col=color_profile[4]) > points(conserved_fluct[,5],type="l",col=color_profile[5]) > points(conserved_fluct[,6],type="l",col=color_profile[6]) > points(conserved_fluct[,7],type="l",col=color_profile[7]) > points(conserved_fluct[,8],type="l",col=color_profile[8]) > conserved_fluct[,1] [1] 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 [56] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 [111] 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 [166] 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 [221] 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 > color_profile = rainbow(dim(fluct)[2]) > layout(matrix([1,2],nrow=2,ncol=1),heights[4,1]) Error: unexpected '[' in "layout(matrix([" > par() $xlog [1] FALSE $ylog [1] FALSE $adj [1] 0.5 $ann [1] TRUE $ask [1] FALSE $bg [1] "transparent" $bty [1] "o" $cex [1] 1 $cex.axis [1] 1 $cex.lab [1] 1 $cex.main [1] 1.2 $cex.sub [1] 1 $cin [1] 0.15 0.20 $col [1] "black" $col.axis [1] "black" $col.lab [1] "black" $col.main [1] "black" $col.sub [1] "black" $cra [1] 10.8 14.4 $crt [1] 0 $csi [1] 0.2 $cxy [1] 6.9468750 0.3348837 $din [1] 7 7 $err [1] 0 $family [1] "" $fg [1] "black" $fig [1] 0 1 0 1 $fin [1] 7 7 $font [1] 1 $font.axis [1] 1 $font.lab [1] 1 $font.main [1] 2 $font.sub [1] 1 $lab [1] 5 5 7 $las [1] 0 $lend [1] "round" $lheight [1] 1 $ljoin [1] "round" $lmitre [1] 10 $lty [1] "solid" $lwd [1] 1 $mai [1] 1.02 0.82 0.82 0.42 $mar [1] 5.1 4.1 4.1 2.1 $mex [1] 1 $mfcol [1] 1 1 $mfg [1] 1 1 1 1 $mfrow [1] 1 1 $mgp [1] 3 1 0 $mkh [1] 0.001 $new [1] FALSE $oma [1] 0 0 0 0 $omd [1] 0 1 0 1 $omi [1] 0 0 0 0 $page [1] TRUE $pch [1] 1 $pin [1] 5.76 5.16 $plt [1] 0.1171429 0.9400000 0.1457143 0.8828571 $ps [1] 12 $pty [1] "m" $smo [1] 1 $srt [1] 0 $tck [1] NA $tcl [1] -0.5 $usr [1] -8.88 257.88 -0.32 8.32 $xaxp [1] 0 250 5 $xaxs [1] "r" $xaxt [1] "s" $xpd [1] FALSE $yaxp [1] 0 8 4 $yaxs [1] "r" $yaxt [1] "s" $ylbias [1] 0.2 > plot(fluct[,1],type="l", lty="dotted",xlab="alignment index", ylab="fluctuations",ylim=c(0,8),col=color_profile[1]) > points(fluct[,2],type="l",lty="dotted",col=color_profile[2]) > points(fluct[,3],type="l",lty="dotted",col=color_profile[3]) > points(fluct[,4],type="l",lty="dotted",col=color_profile[4]) > points(fluct[,5],type="l",lty="dotted",col=color_profile[5]) > points(fluct[,6],type="l",lty="dotted",col=color_profile[6]) > points(fluct[,7],type="l",lty="dotted",col=color_profile[7]) > points(fluct[,8],type="l",lty="dotted",col=color_profile[8]) > points(conserved_fluct[,2],type="l",col=color_profile[1]) > points(conserved_fluct[,3],type="l",col=color_profile[2]) > points(conserved_fluct[,4],type="l",col=color_profile[3]) > points(conserved_fluct[,5],type="l",col=color_profile[4]) > points(conserved_fluct[,6],type="l",col=color_profile[5]) > points(conserved_fluct[,7],type="l",col=color_profile[6]) > points(conserved_fluct[,8],type="l",col=color_profile[7]) > points(conserved_fluct[,9],type="l",col=color_profile[8]) > points(NMP,array(-0.1,dim=length(NMP)),pch=20,col="gray") > points(LID,array(-0.1,dim=length(LID)),pch=20,col="black") > legend("topleft",names+c("NMP domain","LID domain"),fill=colour_profile[1:8]+c("gray","black")) Error in names + c("NMP domain", "LID domain") : non-numeric argument to binary operator > legend("topleft",names+c("NMP domain","LID domain"),fill=colour_profile[1:8]+c("gray","black")) Error in names + c("NMP domain", "LID domain") : non-numeric argument to binary operator > names+c("NMP domain","LID domain") Error in names + c("NMP domain", "LID domain") : non-numeric argument to binary operator > names+"NMP domain","LID domain" Error: unexpected ',' in "names+"NMP domain"," > names<-names+"NMP_domain" Error in names + "NMP_domain" : non-numeric argument to binary operator > names<-paste(name,c("NMP domain","LID domain")) Error in paste(name, c("NMP domain", "LID domain")) : object 'name' not found > names<-paste(names,c("NMP domain","LID domain")) > names [1] "1AK2 A NMP domain" "1AKE A LID domain" "1AKY A NMP domain" "1DVR B LID domain" "2AK3 A NMP domain" "2AKY A LID domain" "2ECK A NMP domain" "4AKE A LID domain" > names<-c("1AK2 A","1AKE A","1AKY A","1DVR B","2AK3 A","2AKY A","2ECK A","4AKE A","NMP domain",LID domain) Error: unexpected symbol in "names<-c("1AK2 A","1AKE A","1AKY A","1DVR B","2AK3 A","2AKY A","2ECK A","4AKE A","NMP domain",LID domain" > names<-c("1AK2 A","1AKE A","1AKY A","1DVR B","2AK3 A","2AKY A","2ECK A","4AKE A","NMP domain","LID domain") > colours<-color_profile[1:8]+c("gray","black") Error in color_profile[1:8] + c("gray", "black") : non-numeric argument to binary operator > colours<-c(color_profile[1:8],"gray","black") > colours [1] "#FF0000FF" "#FFBF00FF" "#80FF00FF" "#00FF40FF" "#00FFFFFF" "#0040FFFF" "#8000FFFF" "#FF00BFFF" "gray" "black" > legend("topleft",cex=0.7,names,fill=colours) >