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Tutorial: MATLAB Basics
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matlab-basics-tutorial.md

Contents

About MATLAB

Elementary Tutorial

External Links

About MATLAB

MATLAB is a numerical computing environment and programming language. Created by The MathWorks, MATLAB allows easy matrix manipulation, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs in other languages. Although it specializes in numerical computing, an optional toolbox interfaces with the Maple symbolic engine, making it a full computer algebra system. It is used by more than one million people in industry and academia and runs on most modern operating systems, including Windows, Mac OS, Linux and Unix. The current version is MATLAB 7.1 Service Pack 3. It is available for commercial use for approximately US$2000 and US$100 for an academic license with a limited set of Toolboxes.
— from Wikipedia:MATLAB

For Bioinformatics and Systems Biology, there are useful toolboxes available:

Elementary Tutorial

The following is an unstructured quick bare bones introduction to some of MATLAB's important commands/functions. MATLAB is reasonably easy to use and intuitive to pick up, so go ahead and experiment and learn!

GENERAL COMMANDS

clc ~ clears the command window clear ~ removes all variables from the workspace clear all ~ removes all variables, globals, functions and MEX links ls ~ Returns listing of the current directory (works on Windows as well) !ls ~ Use ! to run shell commands both in windows and linux. In windows, !explorer . maybe a useful command, to browse the current directory pwd ~ Shows the present working directory (in Windows too) help <command name> ~ gives a brief documentation doc <command name> ~ gives the complete documentation lookfor <text> ~ looks for the string <text> in the first comment line of the HELP text in all M-files (MATLAB functions/scripts) found on <tt>MATLABPATH</tt>. whos ~ It lists all the variables in the current workspace, together with information about their size, bytes, class, etc. whos -file <filename.mat> ~ lists the variables in the specified .MAT file. type <filename> ~ 'cats' or echoes the file to the screen

ESSENTIAL FUNCTIONS

size ~ returns the size of the matrix length ~ returns the maximum dimension of a matrix A' ~ transposes a matrix 1:7:100 ~ Generates numbers upto 100 beginning from 1 in steps of 7.

>> 1:7:100 ans = 1 8 15 22 29 36 43 50 57 64 71 78 85 92 99 >>

linspace ~ linspace(a,b,n) generates n linearly spaced points between a and b logspace ~ generates logarithmically spaced points : ~ (colon) is a wildcard (similar to * in shell). e.g. A(:,4:end). This returns all rows of A and columns from 4 onwards. end is a keyword that tells MATLAB to take elements untill the last column is reached.

Entering a vector

x= [1 2 3 4 5]

Entering a matrix

I_4= [1 0 0 0; 0 1 0 0 ; 0 0 1 0; 0 0 0 1] Instead of a semi-colon, line-breaks (Enter) will also work.

A([1 3 5 7],[2 4 6 8])

any submatrix can be addressed; it can even be assigned a value. For example A([1 3 5 7],[2 4 6 8])=0 sets those elements to zero!

prod(size(x))

a simple construct for calculating the number of elements in x.

find(A)

returns the indices of the non-zero elements in a vector. For matrices, it is better to give two outputs: [i,j]=find(A).

sqrt(i)

complex variables are handled seamlessly. i and j are both square roots of -1. Avoid i,j in loops, therefore.

inline

Can create functions like f(x,y)=\sin(x^2+y^2+xy). e.g.:

>> f=inline('sin(x.^2+y.^2+x.*y)') f = Inline function: f(x,y) = sin(x.^2+y.^2+x.*y)

sparse ~ Use whenever memory problems are possible due to the usage of large matrices. MATLAB intelligently applies the corresponding algorithms. Typically, just saying A=sparse(A) may cause your code to run 10 times faster, if your matrix is large and sparse.

SPECIAL MATRICES

ones(m,n[,p,..]) ~ Generates a matrix of the corresponding size with all elements 1. zeros(m,n) ~ Generates a matrix filled with zeroes; useful for initialisation some times. rand(n) ~ gives an n-by-n matrix with random entries, chosen from a uniform distribution on the interval (0.0,1.0). eye(n) ~ eye(n) is the n-by-n identity matrix. eye(m,n) ~ is an m-by-n matrix with 1's on the diagonal and zeros elsewhere.

Note that a single argument usually creates a square matrix for the above functions.

diag ~ Can be used to extract the diagonal of a matrix or even create diagonal matrices.

INPUT/OUTPUT RELATED

x=1 vs x=1;

suppresses the output

>> x=1 x = 1 >> x=1; >>

disp ~ Suppresses some of the extra lines...

>> x x = 1 >> disp(x) 1 >>

sprintf ~ similar to sprintf of C/++. fprintf ~ similar to fprintf of C/C++. Use either this or sprintf to print on stdout (command window). load ~ loads files. Simplest file is one with equal number of entries in each row separated by space or tab. MATLAB will crib if number of entries in any row are different from others. importdata ~ Useful for loading text files and other files you would usually load using 'File>Import...' xlsread ~ Can read Microsoft Excel files directly save ~ Without filename, all variables are saved to 'matlab.mat'. With filename, all are saved to the corresponding file. You can even specify what variables to save, even with a regular expression! format long ~ Displays many digits of precision (default format shows only 4 decimals) format rat ~ Displays output as rational numbers! format ~ Resets format

MATRIX FUNCTIONS

MATLAB has a host of matrix-related functions. lookfor should come handy for searches.

inv ~ Inverse of a matrix. inv vs \ ~ Inverse of a matrix is expensive to compute and to be avoided. MATLAB supports the beautiful slash operator: Just as for ax=b, x=b/a, even for matrix equations (simulataneous equations), i.e. when \mathbf{A}\mathbf{x}=\mathbf{b} MATLAB allows, x=A\b (try to see it is a b 'over' A!) * ~ Matrix multiplication .* ~ Element-wise multiplication . ~ . does element-wise operations. ~ For example: A^5 vs A.^5: A^5 multiplies A with itself 5 times (matrix product; possible only when A is square) whereas A.^5 raises every element of A to the 5th power. norm ~ Various norms maybe calculated for a matrix. expm(A) vs exp(A) ~ exp(A) does e^{a_{ij}}\ \forall \ a_{ij} \in \mathbf{A}, whereas expm is defined as:

e^\mathbf{A}=\mathbf{I}+\mathbf{A}+\frac{\mathbf{A^2}}{2!}+\frac{\mathbf{A^3}}{3!}+\dots \infty This is of great use while solving systems of differential equations.

svd ~ Singular Value Decomposition eig ~ Eigenvalue/Eigenvector finding chol ~ Cholesky Decomposition

POLYNOMIAL FUNCTIONS

polyval(P,X) ~ returns the value of a polynomial P evaluated at X. P is a vector of length N+1 whose elements are the coefficients of the polynomial in descending powers. Y = P(1)*X^N + P(2)*X^{N-1} + ... + P(N)*X + P(N+1). If X is a matrix or vector, the polynomial is evaluated at all points in X. compan ~ Can be used for solving polynomial equations. Beautiful function! The eigenvalues of the companion matrix of a polynomial are the roots of the polynomial! ~ Example: Calculate the cube roots of unity, i.e. the roots of the equation x^3-1=0:

>> eig(compan([1 0 0 -1])) ans = -0.5000 + 0.8660i -0.5000 - 0.8660i 1.0000 >>

ADVANCED

cell

symbolic

FIGURE RELATED FUNCTIONS

figure ~ Opens a new figure window clf ~ Clears the current figure close ~ Closes the curent figure window close all ~ Closes all figure windows close all hidden ~ Closes all figure windows including those hidden (clustergrams are strangely 'hidden') close (1:gcf) ~ a workaround for closing all including hidden I guess... hold on ~ Holds the current plot on the figure window waitforbuttonpress ~ Waits on the plot during a script/function, till a button is pressed, before further execution subplot ~ Create a grid of plots in a single figure. plot ~ Versatile plot function. ezplot ~ Can plot anything you imagine! Just try ezplot('sin(x*y)')! surf ~ Plots a surface mesh ~ Plots a mesh (similar to surf but ~no solid) title ~ Titles a figure xlabel ~ Add X-Axis title ylabel ~ Add Y-Axis title colormap ~ Change the colours of plots/images spy ~ Sparsity plot of a matrix — puts blue dots wherever entries are non-zero. Shows number of non-zeroes as well.

PROGRAMMING

  • function name and file name should be the same
  • % comments
  • help and comments

help myfun will return the first block of comments in myfun.m

(see the following example as well)

  • return is implicit. For example

% my function to calculate max of two numbers % function a=mymax(x,y) if (x>y) a=x; else a=y' end return %optional: whatever a is at the end of the %function file, that value will be returned.

  • programs vs scripts

Scripts don't have a function keyword. They're just 'scripts', which run a series of commands. The variables are all in memory after the execution of the script

  • if (x~=1)

This is a significant difference from C/C++: instead of x!=1, use x~=1.

  • elseif
  • end - ENDs any blocks - for, if, elseif, while etc (roughly equivalent of } in C++; there is no { if (x~=1) itself implies — loosely— if(x!=1){ of C++))
  • for k=1:100 (not i!!)
  • All addressing is from 1:n
  • handling arguments

Multiple arguments can be specified in the function definition

function [mean,median,mode,variance]=statistics(x)

  • for loops is bad programming... there should be vectorisable alternatives!!

BIOINFORMATICS TOOLBOX

clustergram ~ useful for clustering microarray data etc. Has a lot of options.

SBMLToolBox

External Links

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