lhermida

1. identify a couple (or more) common (bioinformatics) tasks
2. write example apps that help
3. profit!

I think that matplotlib is a bit easier to work with than just about anything in Perl.

It has been a year or three since I last compared plotting libraries to be fair.

As a sysadmin at a university I actually recommend Python (numpy/scipy/matplotlib stack) over Perl (PDL/any plotting package) because most everyone uses Matlab (for good or for bad) and its plotting is rather easy to use.

I still think Perl is probably better overall but without a nicer plotting library (which I suppose I should compare things again) Python is my recommendation.

Chart::Clicker looked really nice and easy to use but was a bit of a pain to get installed properly last I checked (a few years ago).

gizmo

I don't think Chart::Clicker and GD::Graph are not for Scientific plotting.

Perl needs visual attraction like these with independent own project website, not only on CPAN text-only documents.

http://www.rstudio.org/
http://matplotlib.sourceforge.net/gallery.html
http://addictedtor.free.fr/graphiques/allgraph.php

http://groups.google.com/group/perl-scientific-computing is dead ?

Looks like I have a homework assignment this month. :-)

Hopefully I'll have time to digest the informative comments, do a comparison (or at least get a better handle on PDL's plotting) and do a write up.

Also, sounds like a short talk for my monger's group as well.

scipy has own plot library(Matplotlib).
R has own plot library and enhancement(ggplot2)
PDL don't have de facto standard and too many choices.

PGPLOT? its the latest update date is 2002 and oldie fortran code base. Does it promising?
PLPLOT? PDL/Perl can control its future road map?

If PDL can't afford to make a new plotting library, I think that PDL would rather integrate GNUPlot into PDL.

Your best option for using Gnuplot is probably to just print out raw gnuplot commands. You have to tweak the heck out of publication-quality plots, and what are the odds that a Perl wrapper will support the options you need? e.g.

laboff = 0.9
unset log; set auto
set key bot right;
set ylab 'True positives (same superfamily)' laboff,0 font "cmr10,32";
set xlab 'False positives' 0,laboff font "cmr10,32";
set term aqua 1 fname "cmr10" fsize 24; set pointsize 1;set linest lw 5.0
set xtics 0,0.5,1;set ytics 0,0.5,1 # set ylab 1
set xran [0:1];set yran [0:1]
p 'roc-prof-poster.txt' ev 100 t 'Profiles' w linesp pt 9 lt -1, \
'roc-ib-poster.txt' ev 100 t 'IB' w linesp pt 1 lt 1, \
'../poster/roc-cons.txt' ev 100 t 'Consensus' w linesp pt 3 lt 3, x t '' lt 8


What I would like to see are some examples that do some graph work like the following:

1. set up axis with ranges and annotation text
2. plot several data point array with line color choice
3. put multiple cross hairs on the screen in both x and y dirs

I can do this with mathplotlib with about a dozen measly lines of code

Because of this I have been looking at using mathplotlib even though I rather do it in perl.

I've never used Perl so I can't comment on Perl vs. Python, but you missed two critical libraries/tools that Python also brings to scientific computing:

pandas (http://pandas.pydata.org/): offers efficient R-like DataFrames with tons of built-in capability

IPython Notebook (http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html): provides a web-based notebook that enables scientists to log their research in HTML-like cells; embed images, figures, videos, and external web pages; run Python/R/octave code in code cells; and do all kinds of shell commands, data management, data exploration, plotting, etc. -- all in the same tool.

A couple people in my lab were fairly religious about Perl until I showed them IPython Notebook and all the other tools Python has to offer. They switched over without even thinking about it and haven't looked back.

Just a thought from an end-user.

I am not sure what (3) exactly mean. For (1) and (2), Perl can also be done with just few lines. For example, with Chart::Gnuplot, it would be like:

my $chart = Chart::Gnuplot->new(
    output => "test.png",
    xlabel => "x-axis",    # annotation text
    xrange => [0, 10],     # axis range
);

# About data point array 1

my $dataSet1 = Chart::Gnuplot::DataSet->new(

    points => \@data1,

    color  => "blue",      # line color chosen

);

# About data point array 2

my $dataSet2 = Chart::Gnuplot::DataSet->new(

    points => \@data2,

    color  => "dark-red",  # line color chosen

);

$chart->plot2d($dataSet1, $dataSet2);