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comparison snpEff_2_1a/scripts/smoothScatter.pl @ 0:f8eaa3f8194b default tip

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Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author greg
date Fri, 20 Apr 2012 14:47:09 -0400
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1 #!/usr/bin/perl
2 #-------------------------------------------------------------------------------
3 #
4 # Plot a smooth scatter plot
5 # Data is feed as two column of numbers
6 #
7 # Note: Any line that does not match a numeric regular expression, is filtered out).
8 #
9 # Pablo Cingolani
10 #-------------------------------------------------------------------------------
11
12 #-------------------------------------------------------------------------------
13 # Main
14 #-------------------------------------------------------------------------------
15
16 # Parse command line option (file base name)
17 $base = 'smoothScatter';
18 if( $ARGV[0] ne '' ) { $base = $ARGV[0]; }
19
20 $pngFile = "$base.png";
21 $txtFile = "$base.txt";
22
23 # Read STDIN and create an R table
24 open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n";
25 print TXT "x\ty\n";
26 for( $ln = 0 ; $l = <STDIN> ; ) {
27 chomp $l;
28 ($x, $y) = split /\t/, $l;
29
30 # Does the string contain exactly one number? (can be float)
31 if(( $x =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) && ( $y =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ )) { print TXT "$x\t$y\n"; }
32 }
33 close TXT;
34
35 #---
36 # Create an R program, save histogram plot as PNG image
37 #---
38
39 open R, "| R --vanilla --slave " or die "Cannot open R program\n";
40 print R <<EOF;
41
42 smoothLowess <- function( x, y, title, q=1.0 ) {
43 # Show only this part of the data
44 xmin <- quantile( x, 1-q )
45 xmax <- quantile( x, q )
46
47 ymin <- quantile( y, 1-q )
48 ymax <- quantile( y, q )
49
50 keep <- (x >= xmin) & (x <= xmax) & (y >= ymin) & (y <= ymax);
51 qx <- x[ keep ]
52 qy <- y[ keep ]
53
54 smoothScatter(qx, qy, main=title, ylab='Y (column 2)', xlab='X (column 1)');
55 lines( lowess(qx,qy), col='orange' );
56 }
57
58 png('$pngFile', width = 1024, height = 1024);
59 par( mfrow=c(2,1) );
60
61 data <- read.csv("$txtFile", sep='\\t', header = TRUE);
62 x <- data\$x
63 y <- data\$y
64
65 smoothLowess(x, y, "Smooth scatter plot and Lowess", 1.0);
66 smoothLowess(x, y, "Smooth scatter plot and Lowess: Quantile [2% - 98%]", 0.98);
67
68 dev.off();
69 quit( save='no' )
70 EOF
71
72 close R;
73
74 #---
75 # Show figure
76 #---
77
78 $os = `uname`;
79 $show = "eog";
80 if( $os =~ "Darwin" ) { $show = "open"; }
81 `$show $pngFile`;
82