Newbie help with scatter plots in matlab manually & from the unix command line

1. It's hard to help without knowing your exact input file format. Please show at least few lines.
In general, for numeric data only you can use DLMREAD function or CSVREAD. For mixed data, TEXTREAD or TEXTSCAN. You can also use LOAD, IMPORTDATA, etc. Do you have Statistical Toolbox, it has other functions for data import? Where the data came from?

2. Once you import the data, use PLOT function:
plot(x,y,'bo')

3. There are no modules in MATLAB, only scripts, functions, classes and toolboxes as packages. What exactly do you need? Tell us how it going to be run. What is the usage workflow.

4. So do you want a GUI or command line. In the first case use GUIDE to create the GUI. It's easy but definitely will be a little hard for a newbie. You will have to read some documentation, follow tutorials, etc. Probably not a matter for a single question.
As for the command line, I think you get the answer in the previous question.

Lets assume the data file would be in the format below. The first column is the date, the second column is the hour, the third is the observed data, and the fourth/last column is the forecast data. The date and time should be ignored. Lets also assume the file is a txt file or perhaps data file.

10-23-2010 02 0.50 0.00
10-23-2010 14 0.02 0.01
10-24-2010 02 0.00 0.05
10-24-2010 14 0.10 0.03
10-25-2010 02 1.00 0.40
10-25-2010 14 0.00 0.01
10-26-2010 02 0.00 0.02

Here is the code to input the data and make the plot:

filename = 'in.txt';
[obs fcst] = textread(filename, '%*s %*d %f %f');
plot(obs, fcst, 'bd', 'MarkerSize', 3)
xlim([0 4])
ylim([0 4])
axis square
box off
line(xlim, ylim, 'Color', 'k')
xlabel('PW OBS (C)')
ylabel('PW FCST (C)')

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Ok. I need to make sure the forecast range and observation domain for the y & x axis are the same. I may need to adjust them in the future but lets say 25 for so4.txt and 1.00 for so2.txt rounded to whole numbers for so4 or hundredths for so2. How would I write the script for each?

To set axes limits you can use xlim/ylim commands. You can also set axes to be square and equal.

xlim([0 25])
ylim([0 25])
axis square

To change ticks you have to pass ticks vector to axes properties XTick and YTick. gca is your current axes handle.

set(gca,'XTick',0:5:25,'YTick',0:5:25)

Ok. I need to force a 45 degree line instead of a trend line within the plot. How would I do this?

After to make axes limits the same you can do:

line(xlim, ylim, 'Color', 'k')

or you can set line's coordinates directly:

line([0 25], [0 25], 'Color','k')

See here for different line properties:
http://www.mathworks.com/help/techdoc/ref/line_props.html

BTW, all of this were in my original comment: http:#34094347

I am still having difficulties but I will try again.

ok