Compiling matlab to a standalone with no display option

You might often want to compile matlab files to a standalone executable using the mcc command. However, by default you will obtain annoying warning messages about no display being available. To avoid these messages you should use the compiler directive -R

Before Matlab 2010b

mcc -R -nodisplay ...

For Matlab 2010b, although the documentation says it should be the same it isnt. You need to drop the - . i.e.

mcc -R nodisplay ...

isdeployed( )

isdeployed() is a handy function in matlab to check whether a piece of matlab code is running as a standalone deployed app or whether it is running in native matlab.

Truncating or rounding off a decimal value/array to user-specified number of decimal places

Sometimes, you want to truncate long floating point numbers to keep just the first few digits following the decimal point. The easy way to do this is

xr = round(x/n) * n

where
x = original floating point number
n = 10^(-[number of digits after decimal])

e.g. x=1.5673454, n = 0.01 (2 digits after decimal point)
xr = 1.57

Passing data in and out of MATLAB and Python

Came across this great package that allows direct exchange between MATLAB and Python.

http://vader.cse.lehigh.edu/~perkins/pymex.html

How to solve MCR cache access problems on a cluster

Often when I run compiled matlab applications on a cluster, I get the error message

"Could not access the MCR component cache."

This tends to happen because matlab is not able to access the MCE cache directory. By default this happens to be your home directory. When a large number of compiled matlab programs are starting off/running simultaneously (e.g. you submit a job array), the load on the file system is too great giving rise to the problem.

The simplest way to solve this problem, if to point the MCR_CACHE_ROOT environment variable to a local temporary directory on each node on the cluster.

export MCR_CACHE_ROOT=$TMPDIR

This redirects the cache to a temp directory that is able to handle the traffic.

High density scatter plots

The scatter(x,y) function in MATLAB is useful to visualize the joint distribution of two variables x and y. But this function breaks down (gets too slow and memory intensive) if the number of data points in x/y is large.

A nice trick to visualize high density scatter plots is to bin the data and smooth the 2-D histogram. Then one can use the image function or surf function with alpha transparency to view the joint distribution. Darker regions could represent high density of points and light regions could represent low density of points.

R and several other programming languages have built in functions of this. It is a little surprising that MATLAB doesn't have it built in yet. Anyway, here is a paper that gives a very efficient way of creating these smoothed high-density scatter plots and here is an implementation.

PSI-BLAST and BLAST background probabilities

This post is not directly related to MATLAB but I felt it was important to post this.

I recently realized that it is not trivial to find the background amino acid probabilities that are used in BLAST and PSI-BLAST. Google didn't find it. None of the papers referenced in the BLAST papers actually have the frequencies in a tabular form. I would have thought this should have been documented by NCBI in BLAST help or something! Anyway after a few hours of searching and reading papers and eventually code, I found the actual values used. They can be found in this file

http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/tools/blastkar.c

Below are the tables which contain the frequencies. They need to be normalized (divide by the sum of the frequencies = 1000) to convert the frequencies to probabilities.

Google doc spreadsheet

NOTE: PSI-BLAST uses the Robinson values by default

 #if STD_AMINO_ACID_FREQS == Dayhoff_prob
 /*  M. O. Dayhoff amino acid background frequencies   */
 static BLAST_LetterProb Dayhoff_prob[] = {
                 { 'A', 87.13 },
                 { 'C', 33.47 },
                 { 'D', 46.87 },
                 { 'E', 49.53 },
                 { 'F', 39.77 },
                 { 'G', 88.61 },
                 { 'H', 33.62 },
                 { 'I', 36.89 },
                 { 'K', 80.48 },
                 { 'L', 85.36 },
                 { 'M', 14.75 },
                 { 'N', 40.43 },
                 { 'P', 50.68 },
                 { 'Q', 38.26 },
                 { 'R', 40.90 },
                 { 'S', 69.58 },
                 { 'T', 58.54 },
                 { 'V', 64.72 },
                 { 'W', 10.49 },
                 { 'Y', 29.92 }
         };
 #endif

 #if STD_AMINO_ACID_FREQS == Altschul_prob
 /* Stephen Altschul amino acid background frequencies */
 static BLAST_LetterProb Altschul_prob[] = {
                 { 'A', 81.00 },
                 { 'C', 15.00 },
                 { 'D', 54.00 },
                 { 'E', 61.00 },
                 { 'F', 40.00 },
                 { 'G', 68.00 },
                 { 'H', 22.00 },
                 { 'I', 57.00 },
                 { 'K', 56.00 },
                 { 'L', 93.00 },
                 { 'M', 25.00 },
                 { 'N', 45.00 },
                 { 'P', 49.00 },
                 { 'Q', 39.00 },
                 { 'R', 57.00 },
                 { 'S', 68.00 },
                 { 'T', 58.00 },
                 { 'V', 67.00 },
                 { 'W', 13.00 },
                 { 'Y', 32.00 }
         };
 #endif

 #if STD_AMINO_ACID_FREQS == Robinson_prob
 /* amino acid background frequencies from Robinson and Robinson */
 static BLAST_LetterProb Robinson_prob[] = {
                 { 'A', 78.05 },
                 { 'C', 19.25 },
                 { 'D', 53.64 },
                 { 'E', 62.95 },
                 { 'F', 38.56 },
                 { 'G', 73.77 },
                 { 'H', 21.99 },
                 { 'I', 51.42 },
                 { 'K', 57.44 },
                 { 'L', 90.19 },
                 { 'M', 22.43 },
                 { 'N', 44.87 },
                 { 'P', 52.03 },
                 { 'Q', 42.64 },
                 { 'R', 51.29 },
                 { 'S', 71.20 },
                 { 'T', 58.41 },
                 { 'V', 64.41 },
                 { 'W', 13.30 },
                 { 'Y', 32.16 }
         };
 #endif

 static BLAST_LetterProb nt_prob[] = {
                 { 'A', 25.00 },
                 { 'C', 25.00 },
                 { 'G', 25.00 },
                 { 'T', 25.00 }
         };