Lab 3: MATLAB Tutorial
Zhuo Wang
Department of Bioinformatics & Biostatistics
Shanghai Jiao Tong University
(Parts of slides are from Maoying Wu)
MATLAB: Functions
Matrix manipulations
Visualization of data
Implementation of algorithms
Creation of user interfaces
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MATLAB: Layouts
Current Folder
Editor
Command Window
Workspace
Command History
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Using help or doc
help
help command
help on toolbar
doc command
doc query
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Matlab classes: primitives
The three main classes in Matlab are
double: multidimensional array of double precision floating
point numbers
char: multidimensional array of ascii characters
logical: Multidimensional array of 1-bit (0/1) numbers
Eight other built-in primitive classes are
uint8, uint16, uint32, uint64: multidimensional array of 8,
16, 32 or 64-bit, unsigned integers
int8, int16, int32, int64: multidimensional array of 8, 16, 32
or 64-bit, signed integers
Every object in Matlab is a rectangular array, and arrays are at
least 2-dimensional (no notion of 1-d array).
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MATLAB variables
Variables are dynamically typed.
Variable types can be changed
Basic operations
sum, subtract, multiply, divide
power, sqrt, sin, cos, etc.
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Scalars, Vectors and Arrays
1 × 1 arrays are also called scalars.
1 × N arrays are also called row vectors.
N × 1 arrays are also called column vectors
Row and column vectors are called vectors
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Getting Started: Assignment
1 2 1
A= ,b = , Ax = b, x = A−1 b
2 1 2×2
2 2×1
a = [ 1 2; 2 1 ];
a
b = [1;2];
x = a\b
x = inv ( a ) * b
1×1 2×2
A. ∗ A0 = (A is symmetric)
2×2 1×1
a .* a
1×1+2×2 1×2+2×1
A∗A=
2×1+1×2 2×2+1×1
a*a
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Exercise
1
Let π = be the initial probability for two states, and
0
0.8 0.1
T = be the transition probability matrix between
0.2 0.9
states 1 and 2.
pi = [1; 0];
t = [0.8 0.1; 0.2 0.9];
for i =1:20 , pi = t * pi , end
What do you notice? Explain the phenomenon.
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Vector: initialization
x = []; % empty vector
x = [ x rand ]; % append a random element
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Vector: Sorting
% generate 10 uniform random variables
x = rand (10 , 1) ;
% sorting
[y , ind ] = sort (x , ’ ascend ’) ;
% what the indices mean ?
all ( y == x ( ind ) )
% sort the indices
[~ , ind2 ] = sort ( ind , ’ ascend ’) ;
% what the ind2 mean ?
all ( x == y ( ind2 ) )
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Vector: norm
n
xip )1/p
X
||x||p = (
i=1
% generate 10 uniform random variables
x = rand (10 , 1) ;
% l1 - norm
y = norm (x , 1) ;
% how to compute l1 - norm ?
sum ( abs ( x ) ) == y
% l2 - norm
z2 = norm (x , 2) ;
% how to compute the l2 - norm ?
z2 == sqrt ( sum ( x .^2) )
% l - infinity norm
zinf = norm (x , inf ) ;
max ( abs ( x ) ) == zinf
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Vector: Histogram
x = rand (10 , 1) ;
x = x (:) ;
% histogram : the mid of bin and the count in each bin
[ count , mid ] = hist ( x ) ;
% how to get the bin , 10 bins
y = linspace ( min ( x ) , max ( x ) , 11)
all ( y (1:10) + ( y (2) -y (1) ) /2 == mid )
% count
count2 = [];
for i =1:10 , count2 ( i ) = sum (x >= y ( i ) & x <= y ( i +1) ) ; end
% are these two equal ?
all ( count == count2 )
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Special double array
ones(n, m, p)
zeros(n, m, p, q)
rand(n, m)
randn(n, m)
cell(n, m)
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Random array
s = rng ;
A = randn (5) ;
rng ( s )
B = randn (5) ;
A == B
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The size command
If A is an array, then size(A) is a 1 × ndims(A) double array. And
the (1, k) entry is the length of the k th dimension of A.
Examples
A = rand (5 ,6 ,8) ;
B = size ( A ) ;
[ a1 , a2 , a3 , a4 ] = size ( A ) ;
[ a1 , a2 ] = size ( A ) ;
size (A , 2)
size (A , 6)
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The class command
If A is an array, then class(A) is character string, whose value is
the class of A (e.g. double, char, cell, struct, uint32, etc.)
Examples
class ( rand (5 ,6) )
class ( ’ this is a string 1234.56 ’)
class (5==6)
class ( class ( rand (5 ,6 ,8) ) )
class ( cell (4 ,5) )
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Struct array
Like cell arrays, structure arrays (class name is struct) allow
you to group different data types together.
Examples:
student . Name = ’ Fred Smith ’;
student . SID = 12345678;
student . Scores = [62 78 93 61];
size ( student )
class ( student )
fieldnames ( student )
isfield ( student , ’ Name ’)
isfield ( student , ’ Names ’)
student . Scores (3) = 99;
student . Scores ([1 end ])
c = struct ( ’ fld1 ’ , A , ’ fld2 ’ , B ) ;
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File: opening, reading and writing
in_file = fopen ( ’ Name_of_File ’ , ’r ’) ; % read only
if ( in_file == -1)
error ( ’ oops , file can ’t be read ! ’) ;
end
[ number , count ] = fscanf ( file , ’%d ’ , 1) ;
while ( count == 1) % while we have read a number
fprintf ( ’ We just read % s \ n ’ , number ) ;
[ number , count ] = fscanf ( file , ’% d ’ , 1) ; % attempt to
read the next number
end
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fprintf
fprintf ( ’% format \ n ’ , variable ) ;
%s: a string
%c: a single character
%d: a whole number
%f: a floating point number
\n: a newline
\t: a tab
\\: a slash
%%: a percent sign
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Flow control
for loops
while loops
if/elseif/else conditionals
switch/case/otherwise
try/catch
Do NOT forget the end at the end.
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while-loop and for-loop
Listing 1: while-loop
while < condition >
if < something - bad - happens >
break
else
% do something useful
end
% do more things
end
Listing 2: for-loop
for < condition >
if < something - bad - happens >
next
elseif
% do something useful
else
% do something useful
end
% do more things
end
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Graphics in MATLAB
t = 0:.3:10;
y = sin ( t ) ;
plot (t , y ) ;
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3D graphics in MATLAB
[x , y ] = meshgrid ( -2:.2:2 , -2:.2:2) ;
z = x .* exp ( - x .^2 - y .^2) ;
surf (x ,y , z )
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Definition of Functions
function [N , M , Z ] = read_al ignment ( inputfile )
% reads alignment from inputfile , removes inserts and
converts into numbers
align_full = fastaread ( inputfile ) ;
M = length ( align_full ) ;
ind = align_full (1) . Sequence ~= ’. ’ & align_full (1) .
Sequence == upper ( align_full (1) . Sequence ) ;
N = sum ( ind ) ;
Z = zeros (M , N ) ;
for i =1: M
counter = 0;
for j =1: length ( ind )
if ( ind ( j ) )
counter = counter + 1;
Z (i , counter ) = letter2number ( align_full ( i ) .
Sequence ( j ) ) ;
end
end
end
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Functions of the MATLAB Optimization
Linear and Quadratic minimization problems
linprog - Linear programming
quadprog - Quadratic programming
Nonlinear zero finding (equation solving)
fzero - Scalar nonlinear zero finding
fsolve - Nonlinear system of equations solve (function solve)
Linear least squares (of matrix problems)
lsqlin - Linear least squares with linear constraints.
lsqnonneg - Linear least squares with nonnegativity constraints.
Nonlinear minimization of functions:
fminbnd - Scalar bounded nonlinear function minimization.
fmincon - Multidimensional constrained nonlinear minimization.
fminsearch - Multidimensional unconstrained nonlinear minimization, by
Nelder-Mead direct search method.
fminunc - Multidimensional unconstrained nonlinear minimization.
fseminf - Multidimensional constrained minimization, semi-infinite
constraints.
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Linear Programming
Linear programming problem
min f (x) = c T x
s.t.
Ax ≤ a
Bx = b
lb ≤ x ≤ ub;
Objective function: f (x) = c T x
Linear constraints: inequation (Ax ≤ a), equation (Bx = b),
box (lb ≤ x ≤ ub).
[x , fval , exitflag , output , lambda ] = linprog (f , A , a , B , b , lb
, ub , x0 , options ) ;
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Algorithms under linprog
options = optimset ( ’ linprog ’) ;
a simplex algorithm (medium-scale)
options = optimset ( ’ LargeScale ’ , ’ off ’ , ’ Simplex ’ , ’ on ’
);
an active-set algorithm (medium-scale)
options = optimset ( ’ LargeScale ’ , ’ off ’ , ’ Simplex ’ , ’ off
’) ;
a primal-dual interior-point method (large-scale)
options = optimset ( ’ LargeScale ’ , ’ on ’) ;
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Linear programming: Example 1
max 2x1 + 3x2
s.t.
x1 + 2x2 ≤8
2x1 + x2 ≤ 10
x2 ≤3
x1 , x2 ≥0
c = [ -2 , -3] ’;
A = [1 ,2;2 ,1;0 ,1];
a = [8 ,10 ,3] ’;
options = optimset ( ’ linprog ’) ;
options = optimset ( ’ LargeScale ’ , ’ off ’) ;
xsol = linprog (c , A , a , [] , [] , [0 ,0] ’ , [] , [] , options )
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Linear programming: Exercise
1 1 1 1 1 1 10
(A|a) =
5 0 −3 0 1 0 15
1 2 3 0 0 0 5
0 1 2 3 0 0 7
max cT x (B|b) =
0 0 1 2 3 0 8
s.t. 0 0 0 1 2 3 8
Ax =a
3 0 0 0 −2 1 5
(D|d) =
Bx ≥b 0 4 0 −2 0 3 7
Dx ≤d
−2 7 1
lb ≤ x ≤ ub 0 2 −2
−1 2 3
(lb|ub|c) =
−1 3 −4
−5 4 5
1 10 −6
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Linear programming: solution.m
A =[1 ,1 ,1 ,1 ,1 ,1;5 ,0 , -3 ,0 ,1 ,0]; a =[10 ,15] ’;
B1 =[1 ,2 ,3 ,0 ,0 ,0; 0 ,1 ,2 ,3 ,0 ,0;...
0 ,0 ,1 ,2 ,3 ,0;0 ,0 ,0 ,1 ,2 ,3]; b1 =[5 ,7 ,8 ,8]; b1 = b1 (:) ;
D =[3 ,0 ,0 ,0 , -2 ,1;0 ,4 ,0 , -2 ,0 ,3]; d =[5 ,7]; d = d (:) ;
lb =[ -2 ,0 , -1 , -1 , -5 ,1] ’; ub =[7 ,2 ,2 ,3 ,4 ,10] ’;
c =[1 , -2 ,3 , -4 ,5 , -6]; c = c (:) ;
B =[ - B1 ; D ]; b =[ - b1 ; d ];
[ xsol , fval , exitflag , output ]= linprog (c ,A ,a ,B ,b , lb , ub )
fprintf ( ’% s % s \ n ’ , ’ Algorithm Used : ’ , output . algorithm ) ;
disp ( ’ = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ’) ;
disp ( ’ Press Enter to continue ’) ; pause
options = optimset ( ’ linprog ’) ;
options = optimset ( options , ’ LargeScale ’ , ’ off ’ , ’ Simplex ’ , ’ on
’ , ’ Display ’ , ’ iter ’) ;
[ xsol , fval , exitflag ]= linprog (c ,A ,a ,B ,b , lb , ub ,[] , options ) ;
fprintf ( ’% s % s \ n ’ , ’ Algorithm Used : ’ , output . algorithm )
fprintf ( ’% s ’ , ’ Reason for termination : ’)
if ( exitflag )
fprintf ( ’% s \ n ’ , ’ Convergence . ’) ;
else
fprintf ( ’% s \ n ’ , ’ No convergence . ’) ;
end
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User Interface (UI)
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