[R] help with line graphs - rather lengthy to explain need

[Robert D. Bowers M.A.]

I am trying to figure out the best way to organize and plot data 
generated by a Excel spreadsheet (one driving a sample turntable and 
collecting optical spectra).

The output of the equipment and software is an excel spreadsheet with 
sample numbers in the first row, and in the first column there is the 
wavelength in nm.  2048 individual measurements (per wavelength) - 2048 
rows plus the sample number row, and at present I've tested 250 samples, 
with a LOT more to follow.

After I get the spreadsheet, I add a row (just below the sample numbers) 
containing site locations.  I've collected 50 samples per site (each 
assigned a different number), so far 5 sites.  The spreadsheet ends up 
with 2050 rows, 250 columns.

What I want to do is generate a line graph of the data (which could be 
separated out into sections of the optical spectrum), with line colors 
assigned by the site name.  Once that's done, the graphs make sense 
(right now the only way I can do that is using the spreadsheet software, 
and assigning each line the color manually - a very tiresome and 
time-consuming process).

So far, I've tried everything I can to get a graph out using R, without 
luck.  I'm rusty with R and programming... I've used Rcmdr (tried 
transposing data, various settings and so on) and 'played' with ggplot - 
no success.  I'm using Rcmdr to make it easier to work out the bugs, 
then will write a short program to process data.

What I'd like to know is (1) what would be the best way to organize the 
data - sample numbers (cases) in the first row, or in the first column 
with the next row or column being the site name, (2) how would I get 
ggplot to plot the line graph showing all of the samples (number listing 
not important) and all (or a selection) of the different wavelengths, 
while assigning line color based on site name.  Once that's done, I can 
show the within-group vs between-group variation compared to wavelength.

To give an idea of what the data look like:

(name = Longwave)

Sample     34900   34901  34902    34903    34904    (and so on)

Site            Tp         Tc          Cr           Ws Gs

200(nm)    300.5    783.9    101.3      623.8     1385.7

201....

You get the idea.  (maximum measurement value is 4098, the instrument 
takes multiple scans and averages them).

If I can figure this out, it will speed up my work - which I need to do 
so I can get a grant proposal off on time.

Thank you,

Bob

Doctoral Candidate, Applied Anthropology

University of South Florida