[R] Re: RFC: "R::Wrapper" perl module

[Aaron J Mackey]

For those who are interested, a preview version can be obtained at:

http://www.people.virginia.edu/~ajm6q/R-Wrapper-0.01.tar.gz

-Aaron

On Thu, 14 Feb 2002, Aaron J Mackey wrote:

>
> If I actually finished writing this module, would any of you use it?
> Would you wish it did something else/different than what's described
> below?  Any comments or suggestions on its proposed usage, intent, or
> syntax are welcome!  (An alternative, better name would also be
> appreciated)  -Aaron
>
> NAME
>     R::Wrapper - Wrapper around the RS-Perl R module
>
> SYNOPSIS
>       #!/usr/bin/perl -w
>
>       use strict;
>
>       use R::Wrapper qw(:all);
>
>       my @x = 1 .. 10;
>       my @y = 1 .. 10;
>       @x = cumsum(\@x);
>
>       plot( { x => \@x,
>               y => \@y,
>               main => 'Test Plot'
>             }
>           );
>
>       __END__
>
>       # then, at the command line:
>
>       # just view it, nothing else;
>       % ./script.pl
>
>       # after viewing, have the option to save as PDF
>       # (prompt for filename):
>       % ./script.pl --pdf
>
>       # do the same, but specify filenames in advance:
>       % ./script.pl --dump=rawdata.txt
>       % ./script.pl --pdf=testplot.pdf
>       % ./script.pl --ps=testplot.ps
>
>       # only generate the dump, don't preview at all:
>       % ./script.pl --nopreview --pdf=testplot.pdf
>
>       # pipe the postscript to something else:
>       % ./script.pl --ps="| enscript -Pbiochem_LJ5P"
>
>       # the default argument for lpr is -P
>       % ./script.pl --lpr=biochem_LJP
>
>       # send other parameters to lpr (e.g. 2 copies);
>       % ./script.pl --lpr="-Pwrp_ph56 -#2"
>
>       # send pdf's to someone:
>       % ./script.pl --pdf --email=amackey at virginia.edu --subject="Here's the latest version"
>
> DESCRIPTION
>     R::Wrapper is meant to be a utility wrapper around the RS-Perl R module.
>     It currently provides three main features: the first is a visually
>     "cleaner" interface to the R module's calling interface (and handling
>     for a few sticky issues the R module has with vectors versus scalars).
>
>     The second feature is to automatically "annotate" each page of output
>     with meta-information about the script (it's name, path, the date,
>     arguments to the script, etc etc); These annotations will appear at the
>     bottom of the output page, and are meant to aid in the reproduction of
>     the data used by the figure(s) at a later date.
>
>     The third feature is that R::Wrapper provides automatic recognition for
>     --dump, --pdf, --ps, --lpr and --email command line switches to scripts
>     that use R::Wrapper. The point of these switches is that after
>     "previewing" any plotted data in a graphical window, R::Wrapper will
>     automatically prompt the user if they wish to dump the raw numerical
>     data used to generate the plot (--dump), or obtain PDF or postscript
>     (--pdf and --ps, respectively) versions of the plot (including
>     annotations); if a filename was not specified at the command line, or if
>     multiple plots are drawn by the script, the user will be prompted for
>     each necessary filename. Instead of specifying filenames for --dump,
>     --pdf and --ps, the outputs can also be piped into another process.
>     The --lpr option expects arguments to the lpr command, instead of
>     filenames. The --email option is used in conjunction with the other
>     options, and specifies that the outputs should be MIME-attached to an
>     email to be sent to the specified user(s).
>
>     R::Wrapper uses the Getopt::Long module to handle command line options,
>     so scripts that make use of it should 'use R::Wrapper' before any other
>     processing of @ARGV occurs (R::Wrapper will strip out it's specific
>     arguments, leaving any others in @ARGV for processing by the script
>     itself).
>
> MOTIVATION
>     Currently, our research "flow" looks like this:
>
>       1. Generate/collect raw data
>       2. Use Perl scripts to "munge" or otherwise convert raw data into
>          tabular format (or import into a relational database)
>       3. Use R script(s) to analyze, transform and visualize data read in
>          from tabular format (or obtained out of relational database);
>          edit script until the desired output formatting/layout is
>          achieved
>       4. Edit R scripts furiously to redirect plotting output into
>          pdf/postscript/etc.
>       5. Use either Perl or R to (re)generate tabular-formatted plotting
>          data (for import into publication-quality graphing environments)
>
>     R::Wrapper attempts to combine steps 3 through 5 (although it could
>     also be used in a "super script" that performed steps 1 and 2, if
>     desired).  The advantage of doing this is to keep the definitions for
>     data production the same: the same set of Perl and R functions are
>     used to generate "preview" data in step 3, generate hardcopy in step 4
>     and generate export data in step 5.
>
> SUPPORTED ROUTINES
>     Currently, R::Wrapper only supports text output (--dump) for plots
>     generated using the following R functions (as a proof of concept, and
>     because these are the plotting routines we use most often):
>
>     * plot
>     * points
>     * lines
>
> TODO
>
>     * Add some kind of templating mechanism, so that text output can be
>       user-controlled.
>     * Add --dump support for more plotting routines (i.e. 'histogram',
>       'barplot', 'boxplot', etc. etc.).
>
> AUTHOR
>     Aaron J Mackey, amackey at virginia.edu
>
> SEE ALSO
>     perl(1), RS-Perl
>
>

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