Smooth Scatter Plots
On March 24, 2006, Gregor Gorjanc
contributed
an example of how to use the smoothScatter()
function from the Bioconductor
geneplotter package. The blog entry provides links to other resources
for plotting large data sets.
This inspired me to add four examples of
smooth scatter plots to my collection of R scripts.
Recommended: Andrew Gelman’s Blog
Andrew Gelman is a professor in the
Department of Statistics and the Department of Political Science at Columbia University.
He is a coauthor of Applied
Regression and Multilevel Models, by Andrew Gelman and Jennifer Hill;
Bayesian Data
Analysis, 2nd edition, by Andrew Gelman, John B. Carlin, Hal S. Stern, and
Donald B. Rubin; and
Teaching Statistics:
A Bag of Tricks, by Andrew Gelman and Deborah Nolan.
Professor Gelman contributes daily to his blog,
Statistical modeling, causal
inference, and social science: Blog of Andrew Gelman’s research group, featuring
Bayesian statistics, multilevel modeling, causal inference, political science, decision
theory, public health, sociology, economics, and literature (the longest title
that I know of for any blog). I have learned a lot about statistics by reading this blog.
An Old Sierpinski Fractal Drawing Program
I found a copy of the source code for a simple
Motif-based program that draws a Sierpinski fractal. I had written this program in 1998
when I was still doing considerable development using Motif widgets. In order to compile
the program, I had to install
OpenMotif 2.2.3 on my PowerBook.
Stained Glass DNA Helix
The DNA helix that appeared in the upper right corner
of each page on my old web site is made of stained glass and was constructed by my
father-in-law, T. Calvin Cook, of St. Petersburg, Florida.
Patching SSAHA 3.1 (Part 4)
Early this morning I received an e-mail from Adam Spargo at the Wellcome Trust Sanger
Institute. He has placed a link to my SSAHA 3.1 patch on the
SSAHA home page.
Patching SSAHA 3.1 (Part 3)
After about 24 hours of debugging over three days, I found and corrected
the bug that prevented SSAHA from running correctly on a PowerPC Macintosh.
On my web site at
http://sphaerula.com/SSAHA/index.html you will
find a patch file that you can use to update the SSAHA 3.1 source code so it
can be compiled using the GCC 4.0.x compilers available for Mac OS X and
later distributions of Linux (e.g., Fedora Core 4).
Patching SSAHA 3.1 (Part 2)
This is a follow-up to my post on December 29, 2005, about
patching SSAHA 3.1 so it will compile using the GCC 4.0.1 compiler.
I finally got around to compiling the patched version of SSAHA 3.1 using
GCC 4.0.2 under Fedora Core 4. The patched version passes all provided
test programs under Fedora Core 4.
However, under Mac OS X 10.4.4, three of the tests fail. Since the
PowerPC processor uses a different byte ordering than the Pentium
processor, I suspect the problem is in the SSAHA code that deals with
byte ordering. I will continue to investigate since I want to run SSAHA
on a Macintosh.
Details are provided on my web site at
http://sphaerula.com/SSAHA/index.html.
Patching SSAHA 3.1
I attempted to compile SSAHA 3.1 on my Mac OS X computer using the
latest compiler, GCC 4.0.1. Unfortunately, GCC 4.0.1 is much more
finicky about C++ standards than the old GCC 2.95 compiler, and there
were many errors that prevented building the software.
I updated the SSAHA 3.1 code so it would compile using GCC 4.0.1. At the
same time, I fixed all compiler warnings (produced by the GCC -Wall
flag) that I could.
I created and tested a patch file for modifying the SSAHA 3.1 code
so that it can be compiled using GCC 4.0.1 (and, I hope, the GCC 3.3 and
3.4 compilers). I supply the patch file and detailed directions for
using it on my web site at
http://sphaerula.com/SSAHA/index.html.
Using Unicode with Perl
A question in one of the Yahoo Groups about Perl prompted me to learn more about how
Perl handles Unicode. I wrote a complete
example of a Perl script that writes UTF-8 to an output file, then reads from
that file and carries out a regular expression match followed by a substitution.
I added the example to my pages on
intermediate Perl.