Ploting a 2d graph ...Bioinformatics

[govindkailas]

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

[polettix]

Need Help?? You should ask yourself...
• How do I post a question effectively? - ok, that's your data, what do you want to plot exactly?
• How do I compose an effective node title? - it's strange that you ask for 2d graphs when you have at least three coordinates...

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? ...)

[Anonymous Monk]

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.

[polettix]

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.

[jettero]

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.

[eXile]

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>