Gnuplot
A relatively easy way to make graphs from the command line.
I have some information on making nice heatmaps from gnuplot somewhere, but I can't find it right now (I think it is only on my computer at home). --Alex
Here are some sample graphs with the code to make them:
http://chem.skku.ac.kr/~wkpark/tutor/gnuplot/gpdocs/
Here are some more complicated graphs:
http://t16web.lanl.gov/Kawano/gnuplot/intro/index-e.html
Here is how to plot a heatmap (look for "set pm3d map"):
http://t16web.lanl.gov/Kawano/gnuplot/plotpm3d-e.html
And the official site:
http://www.gnuplot.info/
Note that it is incredibly difficult to manually choose which color a line / scatterplot will be in gnuplot. If you figure out how to do this without the intermediate step of editing a postscript file, you should post that information here. It looks like it might be easier in the new gnuplot 4.2:
http://gnuplot.sourceforge.net/demo_4.1/rainbow.html . I don't know if this information also applies to 4.0 (which is what is installed on our machines) or not.
Histograms
If you want to make a histogram from a file with a bunch of values, you should use histogram-R-plot.pl. This Perl script takes a list of numbers and then uses R to plot a histogram. It can also plot multiple data sets on a single scale, if (for example) you wanted to show how two sets were different.
Charlie's R Scripts
Charlie has some R scripts that will take tab-delimited files and make them into nice PDF plots. You can find these in $CVSROOT/cvaske/R/ .
Excel
If you are using excel, and you want to label all the data points on a graph, you can either do it the slow way, or you can download this plug-in and have it done automatically. It takes about 2 minutes to install and figure out how to use the plug-in.
On the mac, you need to first unzip the compressed file, then manually move the "XYChartLabeler.xla" file into (Excel Directory)/Office/Add-Ins/ .
It adds a new item to the "Tools" menu in Excel. If you don't see the new "XY Graph" menu option it, you will have to check the "Add-Ins..." submenu (also under "Tools") and make sure it is checked as "enabled."
-- Main.alexgw - 27 Nov 2006
