Most efficient way of drawing grouped boxplot matlab - matlab

I have 3 vectors: Y=rand(1000,1), X=Y-rand(1000,1) and ACTid=randi(6,1000,1).
I'd like to create boxplots by groups of Y and X corresponding to their group value 1:6 (from ACTid).
This is rather ad-hoc and looks nasty
for ii=
dummyY(ii)={Y(ACTid==ii)};
dummyX(ii)={X(ACTid==ii)}
end
Now I have the data in a cell but can't work out how to group it in a boxplot. Any thoughts?
I've found aboxplot function that looks like this but I don't want that, I'd like the builtin boxplot function because i'm converting it to matlab2tikz and this one doesn't do it well.
EDIT
Thanks to Oleg: we now have a grouped boxplot... but the labels are all skew-whiff.
xylabel = repmat({'Bleh','Blah'},1000,1); % need a legend instead, but doesn't appear possible
boxplot([Y(:,end); cfu], {repmat(ACTid,2,1), xylabel(:)} ,'factorgap',10,'color','rk')
set(gca,'xtick',1.5:3.2:50)
set(gca,'xticklabel',{'Direct care','Housekeeping','Mealtimes','Medication','Miscellaneous','Personal care'})
>> ylabel('Raw CFU counts (Y)')
How to add a legend?

I had the same problem with grouping data in a box plot. A further constraint of mine was that different groups have different amounts of data points. Based on a tutorial I found, this seems to be a nice solution I wanted to share with you:
x = [1,2,3,4,5,1,2,3,4,6];
group = [1,1,2,2,2,3,3,3,4,4];
positions = [1 1.25 2 2.25];
boxplot(x,group, 'positions', positions);
set(gca,'xtick',[mean(positions(1:2)) mean(positions(3:4)) ])
set(gca,'xticklabel',{'Direct care','Housekeeping'})
color = ['c', 'y', 'c', 'y'];
h = findobj(gca,'Tag','Box');
for j=1:length(h)
patch(get(h(j),'XData'),get(h(j),'YData'),color(j),'FaceAlpha',.5);
end
c = get(gca, 'Children');
hleg1 = legend(c(1:2), 'Feature1', 'Feature2' );
Here is a link to the tutorial.

A two-line approach (although if you want to retain two-line xlables and center those in the first line, it's gonna be hackish):
Y = rand(1000,1);
X = Y-rand(1000,1);
ACTid = randi(6,1000,1);
xylabel = repmat('xy',1000,1);
boxplot([X; Y], {repmat(ACTid,2,1), xylabel(:)} ,'factorgap',10)
The result:
EDIT
To center labels...
% Retrieve handles to text labels
h = allchild(findall(gca,'type','hggroup'));
% Delete x, y labels
throw = findobj(h,'string','x','-or','string','y');
h = setdiff(h,throw);
delete(throw);
% Center labels
mylbl = {'this','is','a','pain','in...','guess!'};
hlbl = findall(h,'type','text');
pos = cell2mat(get(hlbl,'pos'));
% New centered position for first intra-group label
newPos = num2cell([mean(reshape(pos(:,1),2,[]))' pos(1:2:end,2:end)],2);
set(hlbl(1:2:end),{'pos'},newPos,{'string'},mylbl')
% delete second intra-group label
delete(hlbl(2:2:end))
Exporting as .png will cause problems...

Related

Matlab Plotting with Labels

I'm trying to plot a knn result from my data, which has 3 columns: x, y , label. There are 3 classes and for each of them I would like to used a different symbol. Here's the way I'm plotting now:
t1 = data(:,3) == 1;
t2 = data(:,3) == 2;
t3 = data(:,3) == 3;
train1 = data(t1,:);
train2 = data(t2,:);
train3 = data(t3,:);
figure(1);
plot(train1(:,1),train1(:,2),'#',train2(:,1),train2(:,2),'*',train3(:,1),train3(:,2),'o');
I want to know if there's a more concise way of doing this. Thanks
Here's the most concise (and working) way to plot your data:
figure(1);
hold all
plot(train1(:,1),train1(:,2),'o')
plot(train2(:,1),train2(:,2),'x')
plot(train3(:,1),train3(:,2),'s')
Here's an example that does what you want in a robust and modular manner. You can easily add classes or modify the figure output.
data = [0.53,0.17,2;0.78,0.60,3;0.93,0.26,1;0.13,0.65,2;0.57,0.69,1;...
0.47,0.75,3;0.010,0.45,1;0.34,0.080,3;0.16,0.23,3;0.79,0.91,3;...
0.31,0.15,1;0.53,0.83,2];
categories = [1,2,3];
symbols = {'s','<','o','d','v','+','x','*'};
figure;
hold all
for loopj = 1:length(categories)
t = data(:,3) == categories(loopj);
train = data(t,:);
label = strcat('Class ',num2str(categories(loopj)));
plot(train(:,1),train(:,2),symbols{loopj},'DisplayName',label,'LineWidth',1.3)
end
lg = legend('show');
lg.Location = 'best';
Use hold all to write on the figure without erasing the previous axi and let Matlab pick line colors.
In any case, you need to manually define the different symbols and each plot command comes with one unique type of line and markers.

How to label graph edges with a loop?

I'm using a for loop to add more nodes and edges on my plot. However, when I add labels on new edges the old labels are removed. I don't know how to keep old edge-labels nor how to store the results of labeledge.
This is what I have got so far.
for r = 1: 10
for j = 1:10
H = addnode(P,nodeName{r}{j});
P = addedge(H, s{r}{j}, t{r}{j}, w{r}{j});
figure;
hold on;
h = plot(P);
labeledge(h,s{r}{j},t{r}{j},labelText{r}{j})
end
end
Every time in the new plot, I can only see the newest cluster of labels while old labels are gone. Ideally, I'd love to hold on the results of labeledge but hold on can't do this. I need to show labels in each step in the loop, thus adding another overall labeledge is not my ideal solution. Any hint would be appreciated.
Edit: All my variables are multiple cells of difference sizes in cell arrays. I use for loop to help to pick up vectors from cells because I don't know how to insert all the levels of information from such cell arrays of cells etc. into addNode function.
The main problem in your code is that you keep plotting the graph again and again. This isn't necessary. Instead, use one loop to create the graph object (G), then plot it all at once, and then use another loop for labeling the graph:
P = graph;
for r = 1: 10
for j = 1:10
P = addedge(P, s{r}{j}, t{r}{j}, w{r}{j});
end
end
h = plot(P);
for r = 1: 10
for j = 1:10
labeledge(h,s{r}{j},t{r}{j},labelText{r}{j})
end
end
If you wish to plot your graph on every iteration, you can use subgraph for that:
for k = 1:height(P.Nodes)
H = subgraph(P,1:k);
figure;
h = plot(H);
c = 1;
out = false;
for r = 1: 10
if ~out
for j = 1:10
if c < k
labeledge(h,c,labelText{r}{j})
else
out = true;
break
end
c = c+1;
end
else
break
end
end
end
Besides that, you should know that (from Matlab documentation):
For the best performance, construct graphs all at once using a single call to graph. Adding nodes or edges in a loop can be slow for large graphs.
Also, regardless of the above recommendation, for an easier manipulation of your data, you should first convert your cells to an array. If your cell array contains a different number of elements in each cell, then it is better to collapse it all to one column:
C = [s{:}]; % and the same for t and w
while any(cellfun(#iscell,C))
C = vertcat(C{:});
end
C = cellfun(#(x) x(:),C,'UniformOutput', false);
S = vertcat(C{:});
Labels = [labelText{:}]; % and the same nodeName
while any(cellfun(#iscell,Labels))
Labels = vertcat(Labels{:});
end
Try to remove the 'figure;' command out of the FOR loop and try to see if this worked.

How to force MATLAB function area to hold on in figure

I'm working on this function which gets axis handler and data, and is supposed to plot it correctly in the axis. The function is called in for loop. It's supposed to draw the multiple data in one figure. My resulted figure is shown below.
There are only two correctly plotted graphs (those with four colors). Others miss areas plotted before the final area (red area is the last plotted area in each graph). But the script is same for every axis. So where can be the mistake? The whole function is written below.
function [] = powerSpectrumSmooth(axis,signal,fs)
N= length(signal);
samplesPer1Hz = N/fs;
delta = int16(3.5*samplesPer1Hz); %last sample of delta frequncies
theta = int16(7.5*samplesPer1Hz); %last sample of theta frequncies
alpha = int16(13*samplesPer1Hz); %last sample of alpha frequncies
beta = int16(30*samplesPer1Hz); %last sample of beta frequncies
x=fft(double(signal));
powerSpectrum = 20*log10(abs(real(x)));
smoothPS=smooth(powerSpectrum,51);
PSmin=min(powerSpectrum(1:beta));
y1=[(smoothPS(1:delta)); zeros(beta-delta,1)+PSmin];
y2=[zeros(delta-1,1)+PSmin; (smoothPS(delta:theta)); zeros(beta-theta,1)+PSmin];
y3=[zeros(theta-1,1)+PSmin; (smoothPS(theta:alpha)); zeros(beta-alpha,1)+PSmin];
y4=[zeros(alpha-1,1)+PSmin; (smoothPS(alpha:beta))];
a1=area(axis,1:beta,y1);
set(a1,'FaceColor','yellow')
hold on
a2=area(axis,1:beta,y2);
set(a2,'FaceColor','blue')
a3=area(axis,1:beta,y3);
set(a3,'FaceColor','green')
a4=area(axis,1:beta,y4);
set(a4,'FaceColor','red')
ADDED
And here is the function which calls the function above.
function [] = drawPowerSpectrum(axesContainer,dataContainer,fs)
size = length(axesContainer);
for l=1:size
powerSpectrumSmooth(axesContainer{l},dataContainer{l},fs)
set(axesContainer{l},'XTickLabel','')
set(axesContainer{l},'YTickLabel','')
uistack(axesContainer{l}, 'top');
end
ADDED 29th July
Here is a script which reproduces the error, so you can run it in your computer. Before running it again you might need to clear variables.
len = 9;
axesContainer = cell(len,1);
x = [0.1,0.4,0.7,0.1,0.4,0.7,0.1,0.4,0.7];
y = [0.1,0.1,0.1,0.4,0.4,0.4,0.7,0.7,0.7];
figure(1)
for i=1:len
axesContainer{i} = axes('Position',[x(i),y(i),0.2,0.2]);
end
dataContainer = cell(len,1);
N = 1500;
for i=1:len
dataContainer{i} = rand(1,N)*100;
end
for l=1:len
y1=[(dataContainer{l}(1:N/4)) zeros(1,3*N/4)];
y2=[zeros(1,N/4) (dataContainer{l}(N/4+1:(2*N/4))) zeros(1,2*N/4)];
y3=[zeros(1,2*N/4) (dataContainer{l}(2*N/4+1:3*N/4)) zeros(1,N/4)];
y4=[zeros(1,3*N/4) (dataContainer{l}(3*N/4+1:N))];
axes=axesContainer{l};
a1=area(axes,1:N,y1);
set(a1,'FaceColor','yellow')
hold on
a2=area(axes,1:N,y2);
set(a2,'FaceColor','blue')
hold on
a3=area(axes,1:N,y3);
set(a3,'FaceColor','green')
hold on
a4=area(axes,1:N,y4);
set(a4,'FaceColor','red')
set(axes,'XTickLabel','')
set(axes,'YTickLabel','')
end
My result of this script is plotted below:
Again only one picture contains all areas.
It looks like that every call to plot(axes,data) deletes whatever was written in axes.
Important note: Do not use a variable name the same as a function. Do not call something sin ,plot or axes!! I changed it to axs.
To solve the problem I just used the classic subplot instead of creating the axes as you did:
len = 9;
axesContainer = cell(len,1);
x = [0.1,0.4,0.7,0.1,0.4,0.7,0.1,0.4,0.7];
y = [0.1,0.1,0.1,0.4,0.4,0.4,0.7,0.7,0.7];
figure(1)
dataContainer = cell(len,1);
N = 1500;
for i=1:len
dataContainer{i} = rand(1,N)*100;
end
for l=1:len
y1=[(dataContainer{l}(1:N/4)) zeros(1,3*N/4)];
y2=[zeros(1,N/4) (dataContainer{l}(N/4+1:(2*N/4))) zeros(1,2*N/4)];
y3=[zeros(1,2*N/4) (dataContainer{l}(2*N/4+1:3*N/4)) zeros(1,N/4)];
y4=[zeros(1,3*N/4) (dataContainer{l}(3*N/4+1:N))];
axs=subplot(3,3,l);
a1=area(axs,1:N,y1);
set(a1,'FaceColor','yellow')
hold on
a2=area(axs,1:N,y2);
set(a2,'FaceColor','blue')
hold on
a3=area(axs,1:N,y3);
set(a3,'FaceColor','green')
hold on
a4=area(axs,1:N,y4);
set(a4,'FaceColor','red')
set(axs,'XTickLabel','')
set(axs,'YTickLabel','')
axis tight % this is to beautify it.
end
As far as I know, you can still save the axs variable in an axescontainer and then modify the properties you want (like location).
I found out how to do what I needed.
len = 8;
axesContainer = cell(len,1);
x = [0.1,0.4,0.7,0.1,0.4,0.7,0.1,0.4];
y = [0.1,0.1,0.1,0.4,0.4,0.4,0.7,0.7];
figure(1)
for i=1:len
axesContainer{i} = axes('Position',[x(i),y(i),0.2,0.2]);
end
dataContainer = cell(len,1);
N = 1500;
for i=1:len
dataContainer{i} = rand(1,N)*100;
end
for l=1:len
y1=[(dataContainer{l}(1:N/4)) zeros(1,3*N/4)];
y2=[zeros(1,N/4) (dataContainer{l}(N/4+1:(2*N/4))) zeros(1,2*N/4)];
y3=[zeros(1,2*N/4) (dataContainer{l}(2*N/4+1:3*N/4)) zeros(1,N/4)];
y4=[zeros(1,3*N/4) (dataContainer{l}(3*N/4+1:N))];
axes=axesContainer{l};
Y=[y1',y2',y3',y4'];
a=area(axes,Y);
set(axes,'XTickLabel','')
set(axes,'YTickLabel','')
end
The area is supposed to work with matrices like this. The tricky part is, that the signal in every next column is not plotted absolutely, but relatively to the data in previous column. That means, if at time 1 the data in first column has value 1 and data in second column has value 4, the second column data is ploted at value 5. Source: http://www.mathworks.com/help/matlab/ref/area.html

How do I format a MATLAB figure text annotation into rows and columns?

I have a script which fits some optical data to a sum of Lorentzian oscillators, and then spits out a figure with the original data and the fit. I would also like to include a text annotation with a table of the fitting parameters, but cannot figure out how to get rows and columns in my text box.
Each peak has 3 parameters and then there are 3 more global fitting parameters. My first try was to do this:
ParamTableLabels = {'\omega_p (cm^{-1})', '\omega_0 (cm^{-1})', '\Gamma (cm^{-1})'};
ParamTableVals = num2cell(Ef);
ParamTableLabels2 = {'d (\mu{m})','\epsilon_\infty','Scale'};
ParamTableVals2 = {ThickFit,EinfFit,ScaleFit};
ParamTable = vertcat(ParamTableLabels,ParamTableVals,ParamTableLabels2,ParamTableVals2);
where Ef is my 3xN matrix of fitting parameters. After generating my figure, I try to place the table in my plot at a suitable set of coordinates X,Y using:
text(X,Y,ParamTable)
and the result is a single column of text, no rows. My second attempt, which sort of works is to break up each column:
text(X, Y,ParamTable(:,1));
text(X+dX, Y,ParamTable(:,2));
text(X+2*dX,Y,ParamTable(:,3));
This almost works, but the subscripts in the labels throw off the vertical alignment of the last few rows, and it takes an undue amount of tinkering to get the spacing correct. I'm spending more time trying to get the text box to look right than to do the actual modelling.
How can I programatically format a block of text, containing both labels and variables, into rows and columns, and then use it as a text annotation in a figure with minimal user tinkering?
This is a not well supported using basic commands. But you can at least save yourself the trouble of guessing the subsequent X positions by making Matlab do the work for you.
The key is the "Extent" read-only parameter attached to a text block. Use docsearch text properties to see the documentation.
Putting this into some code:
padFraction = 0.1; %This is roughly the unitless padding between columns, as a fraction of the column on the left.
curX = X; %Leave the initial X variable unchanged
%For each text block column, add the text block, get the extent, and adjust curX
h = text(curX, Y,ParamTable(:,1));
curExtent = get(h, 'Extent');
curX = curExtent(1) + curExtent(3)*(1+padFraction);
h = text(curX, Y,ParamTable(:,2));
curExtent = get(h, 'Extent');
curX = curExtent(1) + curExtent(3)*(1+padFraction);
text(curX,Y,ParamTable(:,3));
The full script used to generate/test is below:
ParamTableLabels = {'\omega_p (cm^{-1})', '\omega_0 (cm^{-1})', '\Gamma (cm^{-1})'};
Ef = round(rand(10,3)*100);
ParamTableVals = num2cell(Ef);
ParamTableLabels2 = {'d (\mu{m})','\epsilon_\infty','Scale'};
ParamTableVals2 = {'ThickFit','EinfFit','ScaleFit'};
ParamTable = vertcat(ParamTableLabels,ParamTableVals,ParamTableLabels2,ParamTableVals2);
X = 1; Y = 1.1;
%Put something in the plot
figure(1); clf; hold on;
plot(-10:10, randn(21,1)*20,'.');
codeblock = 3;
switch codeblock
case 1
text(X,Y,ParamTable)
case 2
dX = 3;
text(X, Y,ParamTable(:,1));
text(X+dX, Y,ParamTable(:,2));
text(X+2*dX,Y,ParamTable(:,3));
case 3
padFraction = 0.1;
curX = X;
h = text(curX, Y,ParamTable(:,1));
curExtent = get(h, 'Extent');
curX = curExtent(1) + curExtent(3)*(1+padFraction);
h = text(curX, Y,ParamTable(:,2));
curExtent = get(h, 'Extent');
curX = curExtent(1) + curExtent(3)*(1+padFraction);
text(curX,Y,ParamTable(:,3));
end

MATLAB - Labeling Curves During Iteration

I want to show the p value that was used to generate each curve next to each of the curves plotted. Note that since there is a plot of E and -E, the same p value should be next to both. I've been attempting this for a while and I have not come across anything super useful.
t = -3.1;%coupling
a = 1;%distance between r1 and r3
n = 5;%latice vector span in a1 direction
m = 1;%latice vector span in a2 direction
i = -7;%unique axial vector t_hat direction
j = 11;%unique axial vector c_hat direction
max_p = abs((n*(i+j/2)-j*(m+n/2)));%# of unique p values
La = sqrt(3)*sqrt(m^2+n*m+n^2)*a/gcd(2*n+m,2*m+n);%unit cell length
C = sqrt(n^2+n*m+m^2);%circumference of the nanotube
hold on;
for p=0:1:max_p
kt = -pi/La:.05:pi/La;
kc = 2*pi*p/C;
ka1 = kc*a*.5*(2*n+m)/C + kt*a*sqrt(3)*.5*m/C;
ka2 = kc*a*.5*(n+2*m)/C - kt*a*sqrt(3)*.5*n/C;
E = abs(t+t*exp(1i*ka2)+t*exp(1i*ka1));
title_ = sprintf('(%d,%d) Carbon Nanotube Dispersion Diagram',n,m);
title(title_);
xlabel('k_{t}a');
ylabel('Energy (eV)');
plot(kt,E);
plot(kt,-E);
end
There is a command named text that writes comments into the figures,
http://www.mathworks.se/help/techdoc/ref/text.html
with if you can't solve it with that and the to string operation i misunderstood the question
First, do you need to plot both E and -E? Since these are the same except for their sign you don't really add any information to the plot by having -E there as well. However, if you do need both lines, then just construct an array of strings for the legend, during the loop, which has each string included twice (once for E and once for -E).
... Initial calculations ...
hold on;
for p=0:1:max_p
kt = -pi/La:.05:pi/La;
kc = 2*pi*p/C;
ka1 = kc*a*.5*(2*n+m)/C + kt*a*sqrt(3)*.5*m/C;
ka2 = kc*a*.5*(n+2*m)/C - kt*a*sqrt(3)*.5*n/C;
E = abs(t+t*exp(1i*ka2)+t*exp(1i*ka1));
plot(kt,E);
plot(kt,-E);
% Construct array containing legend text
legend_text{2*(p+1)-1} = strcat('p=', num2str(p));
legend_text{2*(p+1)} = strcat('p=', num2str(p));
end
title_ = sprintf('(%d,%d) Carbon Nanotube Dispersion Diagram',n,m);
title(title_);
xlabel('k_{t}a');
ylabel('Energy (eV)');
legend(legend_text)
I am sure there is a more elegant way of constructing the legend text, but the above code works. Also, notice that I moved the calls to xlabel, ylabel and title to outside of the loop. This way they are only called once and not for each iteration of the loop.
Finally, you need to take care to ensure that each iteration of the loop plots with a different line colour or line style (see edit below). You could colour/style each pair of E and -E lines the same for a given iteration of the loop and just display the legend for E (or -E), which would obviously halve the number of legend entries. To do this you will need to hide one of line's handle visibility - this prevents it from getting an item in the legend. To do this use the following in your loop:
plot(kt, E);
plot(kt,-E, 'HandleVisibility', 'off');
% Construct array containing legend text
legend_text{p+1} = strcat('p=', num2str(p));
Finally, it is best to include clear all at the top of your Matlab scripts.
Edit: To have each plotted line use a different colour for each iteration of your loop use something like the following
... initial calculations ...
cmap = hsv(max_p); % Create a max_p-by-3 set of colors from the HSV colormap
hold on;
for p = 0:1:max_p
plot(kt, E, 'Color', cmap(p,:)); % Plot each pair of lines with a different color
plot(kt, -E, 'Color', cmap(p,:));
end