Simple Matlab/Octave Commands to Process Data

To load data in following format stored in a text file "read_pos' into Matlab/Octave, use commands<br />

f=fopen('read_pos','r'); % open file
a=textscan(f,'%s%d');  % read file
y=a{2}; % a is a cell: a{1} stores read id, a{2} stores numbers.

Then data of the second column are stored in variable y.

r12353.1 	2407054.5
r12361.1 	5328858.5
r12363.1 	2360272
r12368.1 	4726440.5
r12372.1 	2224001
r12373.1 	5165613.5
r12381.1 	501776
r12385.1 	3475398
r12394.1 	3376364
r12401.1 	2142875.5
r12411.1 	2191090.5
r12419.1 	1240590
r12420.1 	4903572
r12422.1 	767011.5
r12426.1 	3575915.5
r12429.1 	554956
r12433.1 	4786335
r12435.1 	3373955.5
r12442.1 	5363611.5
r12452.1 	1903660.5
r12454.1 	2784165
r12466.1 	5137479
r12470.1 	592191

If there are only numbers stored in file "read_pos", following commands should be used:

f=fopen('read_pos','r'); % open file
a=textscan(f,'%s%d');  % read file
y=cell2mat{a}; % convert cell a to vector
size(y) % check the size

To plot the distribution of all the numbers, you can:

x=zeros(size(y));
plot(y,x,'bo');

If another data set z is also loaded and you want to plot y and z in the same graph, you can:

figure
x=zeros(size(y));
plot(y,x,'bo');
hold on
x=ones(size(z));
plot(z,x,'r+');

To annotate and scale the graph, use commands;

xlabel('AMD Data k-mer Occurrances');
title('GPD Classification of AMD k-mers')
legend('Bin 1','Bin 2')
axis([-5 5 0 10000]) % scale axes

A matlab function to plot multiple datasets:

function result=plot_distr(varargin)

nVarargs=length(varargin);

marker={'bo' 'r+' 'k*' 'gs' 'y^' 'md' 'cp' 'bx' 'r.' 'k>' 'gh' 'y<'};
figure
for k=1:nVarargs
f=fopen(varargin{k},'r');
a=textscan(f,'%d');
y=cell2mat(a);
x=zeros(size(y))+k;
plot(y,x,marker{k});
hold on
end
ylim([0-5*nVarargs 6*nVarargs]); % scale y-axis

To use it, call

plot_distr('file1','file2',...,'filen').