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Ploting a 2d graph ...Bioinformatics

by govindkailas (Acolyte)
on Apr 27, 2007 at 10:15 UTC ( #612346=perlquestion: print w/ replies, xml ) Need Help??
govindkailas has asked for the wisdom of the Perl Monks concerning the following question:

i have set of values of XYZ coord and the result of their RMSD(root mean square deviation),all these are stored in a file... so i need to plot a graph by reading this values from the file.the file content is shown below
X Y Z coords for model:1 X Y Z coords for model:2 Distance btwn the +coords ******************** ******************** ************** +****** 3.434 -6.163 -1.655 3.853 -6.638 -1.842 0.660420320704 +928 -6.227 0.621 3.115 -6.323 0.008 3.458 0.708966853950 +169 -1.324 -1.345 -3.901 -1.134 -1.015 -3.797 0.394735354383 +161 5.781 2.099 4.597 5.506 2.312 5.263 0.751365423745 +33 4.926 6.887 -2.229 5.453 6.881 -2.623 0.658028114900 +876 -5.284 -1.264 -0.084 -4.929 -1.189 0.099 0.406372981385 +327 6.096 4.124 -4.591 6.379 3.890 -4.817 0.431185574897 +862 *********************************** X Y Z coords for model:1 X Y Z coords for model:3 Distance btwn the +coords ******************** ******************** ************** +****** 3.434 -6.163 -1.655 3.355 -6.081 -2.184 0.541115514469 +877 -6.227 0.621 3.115 -6.412 0.418 3.323 0.344525761010 +697 -1.324 -1.345 -3.901 -1.189 -1.065 -3.601 0.432001157405 +857 5.781 2.099 4.597 5.448 2.564 5.351 0.946377303193 +604 4.926 6.887 -2.229 5.132 6.599 -2.797 0.669331009292 +114 -5.284 -1.264 -0.084 -4.933 -0.678 -0.034 0.684906562970 +454 X Y Z coords for model:1 X Y Z coords for model:4 Distance btwn the +coords ******************** ******************** ************** +****** 3.434 -6.163 -1.655 3.845 -6.488 -1.926 0.589904229515 +266 -6.227 0.621 3.115 -5.952 1.213 3.659 0.849720542296 +113 -1.324 -1.345 -3.901 -1.273 -1.053 -3.983 0.307553247422 +296 5.781 2.099 4.597 5.848 1.551 5.892 1.407770577899 +68 4.926 6.887 -2.229 5.103 6.729 -2.644 0.478035563530 +581 -5.284 -1.264 -0.084 -5.233 -0.566 0.355 0.826151317858 +902
how can i plot this??? can any one help me plzz

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Re: Ploting a 2d graph ...Bioinformatics
by jettero (Monsignor) on Apr 27, 2007 at 10:53 UTC

    I'm fond of using gri for plotting — particularly for technical papers. That has nothing to do with perl of course...

    In perl, I'd almost certainly use GD::Graph for the plotting and I'd use regular expressions to read the values into my @data = ( [@X], [@Y1], [@Y2], [@Y3], ... ) array.

    -Paul

Re: Ploting a 2d graph ...Bioinformatics
by polettix (Vicar) on Apr 27, 2007 at 11:06 UTC
    Need Help?? You should ask yourself...

    On a general basis, for the plotting part, first decide what you're interested to plot, then take a look at GD::Graph and GD::Graph3D.

    To read the data, you can open the file, then iterate on its lines - something like this:

    open my $fh, '<', $filename or die "open('$filename'): $!"; while (<$fh>) { # Do whatever you want with the line in $_ } close $fh;
    Before going further, again, you must decide what you want to plot and how (e.g. you have three datasets: do you want a graph for each of them? Do you want to mix up all data? ...)

    Flavio
    perl -ple'$_=reverse' <<<ti.xittelop@oivalf

    Don't fool yourself.
      GD::Graph can't make 2D data plots. It will only take a series of Y-values, and display them left-to-right in the order given. There's no way, for instance, to make a plot in which there are 2 points with the same X value - at least, no way I can discover.
        This is unbelievable. Don't know where you tried to discover how to do it, but the very first example in GD::Graph documentation shows you how to:
        • set your own X axis values/labels, AND
        • plot two graphs in a single chart.

        Flavio
        perl -ple'$_=reverse' <<<ti.xittelop@oivalf

        Io ho capito... ma tu che hai detto?
Re: Ploting a 2d graph ...Bioinformatics
by eXile (Priest) on Apr 27, 2007 at 14:35 UTC
    I'd second the posts above, but can't resist plugging another option for actually plotting your data once you have selected the data you want to plot:

    <shameless plug> Chart::Graph::Gnuplot </shameless plug>

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