I have some points in a 'jet' colormap. The points have a coefficient that can go from 0 to 1, but usually they dont cover all the range, e.g 0.75-0.9.
When I plot those points I colour them so 0.75 is the lesser colour in the colormap and 0.9 is the maximum color in the colormap, so all the colormap is shown. What I want to do is show that in the colorbar also. When I plot the colorbar the labels on it go to 64, but I want them from 0.75 to 0.9. How can I do that?
EDIT
I don't think the code itself helps a lot but here it goes, just in case. In the colors variable I convert the ZNCC to the range of the colormap.
EDIT2
I found the reason why caxis is not working for me. Here is the code:
%this is why it doesnt work
im=imread('someimageyouwanttotest_inRGB.png')
imshow(im)
points=[1, 2;1 , 2 ;0.3,0.7]
ZNCC=points(3,:)
cmap=colormap('jet');
colors=cmap(round( ((1-min(ZNCC))+ZNCC-1).*(size(cmap,1)-1)/max((1-min(ZNCC))+ZNCC-1))+1,: );
hold on
for i=1:length(ZNCC)
plot(points(1,i),points(2,i),'.','Color',colors(i,:));
end
colorbar()
hold off
I think that is your code displays all your colours correctly then rather just set up the colour bar first on no image:
points=[1, 2;1 , 2 ;0.3,0.7]
ZNCC=points(3,:)
cmap=colormap('jet');
caxis([min(ZNCC) max(ZNCC)]);
colorbar();
hold on
%this is why it doesnt work
im=imread('someimageyouwanttotest_inRGB.png')
imshow(im)
colors=cmap(round( ((1-min(ZNCC))+ZNCC-1).*(size(cmap,1)-1)/max((1-min(ZNCC))+ZNCC-1))+1,: );
for i=1:length(ZNCC)
plot(points(1,i),points(2,i),'.','Color',colors(i,:));
end
hold off
I can't test it as I don't have imshow :/
If caxis is not working for you, you could store the return from colorbar - it is a handle to the colorbar object. Then you can set its properties, like 'YTick' and 'YLim'. The full list of properties you can set is the same as the Axes Properties (because the colorbar is just an axes object, after all).
Here is an example:
% Generate some random data
z = rand(10);
[x, y] = meshgrid(1:size(z, 1));
% Plot colour map
pcolor(x, y, z);
shading interp; % Comment out to disable colour interpolation
colormap jet;
% Setup colorbar
c = colorbar();
set(c, 'YTick', [0.75 0.875 1]); % In this example, just use three ticks for illustation
ylim(c, [0.75 1]);
It is only necessary to do this once, after you've finished plotting.
Edit: If you need the limits and ticks automatically from the data, then you can do something like
% Find the limits
lims = [min(z(:)) max(z(:))];
% Function for rounding to specified decimal places
dprnd = #(x, dps)round(x*(10.^dps))./(10.^dps);
% Generate ticks
nTicks = 5;
nDps = 2;
ticks = dprnd(linspace(lims(1), lims(2), nTicks), nDps);
set(c, 'YTick', ticks);
Related
I have datasets for 5 different frequencies in a matrix and I want to illustrate them using plot, hist and mesh. However, each plot type is using different colormaps (see picture), so I need a legend for every plot.
Is there a way to set the same colormap for all plot types, or specify one for each of them? Another thing thats strange: I can set the colormap for hist using the figure tools for example, but not for the normal plot. For the mesh I have to use a hold on loop, so I guess setting the color here is different from defining a colormap?
Edit:
Here is a minimal example. Its still not working, see comments in the code below.
clear all;
close all;
clc;
% make up some data with the original format
freqLen = 5;
data = zeros(10, 3, 3, freqLen);
data(:, :, :, 1) = rand(10, 3, 3);
data(:, :, :, 2) = rand(10, 3, 3)+1;
data(:, :, :, 3) = rand(10, 3, 3)+2;
data(:, :, :, 4) = rand(10, 3, 3)+3;
data(:, :, :, 5) = rand(10, 3, 3)+4;
% reshape data so we get a vector for each frequency
dataF = reshape(data, [10*3*3, freqLen]);
% prepare colors for plot, try to get 5 colors over the range of colormap
% but I get wrong colors using both methods below!
%cols = colormap(jet);
%cols = cols(1:round(length(cols)/length(freqGHz)):end, :);
cols = jet(freqLen);
% plot samples in 3D
figure('Position', [0 0 1000 1000]);
subplot(211);
hold on;
for iF = 1:freqLen
dataThisF = dataF(:, iF);
data3D = reshape(dataThisF, [10*3, 3]);
mesh(data3D);
% try to give each "holded" mesh a different color. Not working!
% after the loop, all meshes have the last color
set(get(gca, 'child'), 'FaceColor', 'w', 'EdgeColor', cols(iF, :));
end
view(60, 20);
% plot samples
subplot(223);
hold on;
for iF = 1:freqLen
% the loop is not avoidable
% because matlab maps the colors wrong when plotting as a matrix
% at least its not using the colormap colors
plot(dataF(:, iF), 'Color', cols(iF, :));
end
% plot histogram
subplot(224);
% actually the only one which is working as intended, horray!
hist(dataF, 50);
How can I give a holded mesh a single color, different from the others? How can I map the correct jet colormap when plotting a matrix using simple line plot, or at least get 5 colors from the jet colormap (jet(5) give 5 different colors, but not from start to end)?
What you are talking about is mainly the ColorOrder property (and not the colormap of the figure).
The link for the colororder given just above will explain you how to force Matlab to use a given set of colors for all the plots. It works perfectly fine for plot. You wouldn't need a loop, just define the DefaultColororder property of the figure before the plots then plot all your series in one single call, Matlab will assign the color of each plot according to the order you defined earlier.
For mesh and hist it is not that simple unfortunately, so you will have to run a loop to specify the color or each graphic object. To modify a graphic object property (like the color) after it has been created, you have to use the set method, or even the direct dot notation if you're using a Matlab version >= 2014b. For both methods you needs to have the handle of the graphic object, so usually the easiest when you know you'll need that is to retrieve the graphic object handle at the time of creation*.
*instead of dirty hack like get(gca, 'child'). This is quite prone to errors and as a matter of fact was wrong in your case. Your code wouldn't color properly because you were not getting the right graphic handle this way.
The code below plots all your graphs, retrieve the handle of each graphic object, then assign the colors in the final loop.
%// Get a few colors
cols = jet(freqLen);
% plot samples in 3D
figure('Position', [0 0 1000 1000]);
set( gcf , 'DefaultAxesColorOrder',cols) %// set the line color order for this figure
subplot(2,1,1,'NextPlot','add'); %// 'NextPlot','add' == "hold on" ;
for iF = 1:freqLen
dataThisF = dataF(:, iF);
data3D = reshape(dataThisF, [10*3, 3]);
h.mesh(iF) = mesh(data3D) ; %// plot MESH and retrieve handles
%// You can set the color here direct, or in the last final "coloring" loop
%// set( h.mesh(iF) , 'FaceColor', 'w', 'EdgeColor', cols(iF, :));
end
view(60, 20);
%// plot samples
subplot(223);
h.plots = plot(dataF); %// plot LINES and retrieve handles
%// plot histogram
subplot(224);
[counts,centers] = hist(dataF, 50 ) ; %// get the counts values for each series
h.hist = bar(centers,counts) ; %// plot HISTOGRAM and retrieve handles
%// now color every series with the same color
for iF = 1:freqLen
thisColor = cols(iF, :) ;
set( h.mesh(iF) , 'EdgeColor' , thisColor , 'FaceColor', 'w' );
set( h.hist(iF) , 'EdgeColor' , thisColor , 'FaceColor' , thisColor )
%// this is actually redundant, the colors of the plots were already right from the
%// beginning thanks to the "DefaultColorOrder" property we specified earlier
set( h.plots(iF) , 'Color' , thisColor )
end
Will land you the following figure:
UPDATE: The original question asked
Is there a way to set the same colormap for all plot types, or specify one for each of them?
this answer, answers that question with colormap taken to mean colormap in MATLAB literally.
You can set the colormap for a figure using colormap. You could use one of the many built in colormaps or specify your own.
An example using mesh and the builtin hsv colormap could be
figure;
mesh(data);
colormap(hsv);
This would apply a colormap based on
to your figure. You can also create your own colormap like
map = [1, 0, 0,
1, 1, 1,
0, 1, 0,
0, 0, 0];
colormap(map);
which would create a colormap with the colours Red, White, Blue and Black.
The MATLAB documentation contains extensive information on the use of colormap.
Environment: Windows 7 64 bit, Matlab 2014a
Objective:
To draw a heatmap of errors for two parameters to be optimized.
To put proper tick marks and tick values
Draw the grid lines in the correct place
Problem: Arranging the X and Y tick positions and values. When the last ("end") value of the vectors in x and y axes are the same, the code I use puts the ticks and values properly. However, when the end values are different it does not, and produces something really weird.
Below I have included the code which I have modified so that you can run it without the need of adding anything. Of course in my case the error vector are the error values, not random numbers. To see the problem of "end value" use the second b vector.
fontsize = 20
k = [2^-5, 2^-3, 2^-1, 2^0, 2^1, 2^3, 2^5, 2^7, 2^9, 2^11, 2^13, 2^15]
b = [2^-5, 2^-3, 2^-1, 2^0, 2^1, 2^3, 2^5, 2^7, 2^8, 2^9, 2^10, 2^11, 2^13, 2^15]
% b = [2^-5, 2^-3, 2^-1, 2^0, 2^1, 2^3, 2^5, 2^7, 2^8, 2^9, 2^10, 2^11, 2^13, 2^19]
errorVector = randi(20, 1, length(b)*length(k))'
figure
% Create a matrix from error vector (size of error vector is [length(k)*length(b),1])
B = reshape(errorVector, [length(b), length(k)])
B = flipud(B)
% imagesc(x,y,C)
imagesc(b, k, B)
title('Heatmap Parameters Percent Error', 'FontSize', fontsize);
% Set colorbar limits
caxis([0 15])
colorbar;
ax1 = gca;
xTickLabel = (k)'
xTick = linspace(k(1), k(end), numel(xTickLabel))';
set(ax1, 'XTick', xTick, 'XTickLabel', xTickLabel)
xlabel('k parameter', 'FontSize', fontsize)
yTickLabel = (b)'
yTick = linspace(b(1), b(end), numel(yTickLabel))';
set(ax1, 'YTick', yTick, 'YTickLabel', flipud(yTickLabel(:)))
ylabel('b parameter', 'FontSize', fontsize)
set(ax1,'FontSize', fontsize)
Here, change any of the end values of b or k vectors, and the program will output a graph where the X and Y ticks are totally wrong.
Also, I would like to draw grid lines. When I use "grid on" it draws grid lines right on the tick marks which is not correct in the case of heatmap. Because tick marks will be in the center of the columns -or rows- but the grid lines should be at the boundaries between the columns -or rows.
By the way if you know a better way to plot a heatmap in Matlab, please do tell.
Please help me solve this problem. Any help is appreciated,
Ilyas
First of all - you don't need to flipud the B matrix - by default imagesc plots the y-data inversed, but you can fix this with the following statement:
set(gca,'ydir','normal');
This also means you don't have to mess around with flipping the tick-labels. You can get the labels right by doing the following:
% replace the imagesc call with:
imagesc(B);
set(gca,'ydir','normal');
% formatting stuff
...
% replace the set commands with:
set(ax1, 'XTick', 1:length(k), 'XTickLabel', k)
set(ax1, 'YTick', 1:length(b), 'YTickLabel', b)
By default, if you don't provide x and y data to the imagesc command, it will number them linearly (1,2,3...). Basically what we've done here is make sure that it has ticks for each of the elements of b and k, and then set the labels to the values of the respective vectors.
Unfortunately, I'm not sure if there is a way to get the grid spacing right with imagesc or not. You could try using pcolor instead, which has it's own set of issues, but allows you to get grid lines (of sorts) between the elements. It also allows you to use an interpolated shading mode, which will make your plot look more like a typical heat map.
To use pcolor instead, you just have to replace imagesc:
% imagesc(B);
% set(gca,'ydir','normal');
pcolor(B);
% this uses a smoother shading method, for a more 'heatmap' like output
% shading interp
Everything else should work as intended, I believe.
I'm trying to emulate this graph:
If I have a correlation matrix how can I create an output like this?
If you have an n x n correlation matrix M, and a vector L of length n containing the label for each bin, you can use something like the following:
imagesc(M); % plot the matrix
set(gca, 'XTick', 1:n); % center x-axis ticks on bins
set(gca, 'YTick', 1:n); % center y-axis ticks on bins
set(gca, 'XTickLabel', L); % set x-axis labels
set(gca, 'YTickLabel', L); % set y-axis labels
title('Your Title Here', 'FontSize', 14); % set title
colormap('jet'); % set the colorscheme
colorbar on; % enable colorbar
Rotating x-axis labels is not trivial, but the MATLAB Central File Exchange contains some solutions.
Adding to #Thomas C. G.'s answer, I'd use:
imagesc(myMatrix);
colormap(jet);
colorbar;
% then to set the axis titles you'll have to use
% Please note the curly braces for the cell array
labelNames = {'USA','NASDAQ','Dow Jones'};
set(gca,'XTickLabel',labelNames); % gca gets the current axis
set(gca,'YTickLabel'labelNames); % gca gets the current axis
Unfortunately, AFAIK, making the text labels vertical as they are in your figure is a bit harder. Maybe somebody else has knowledge to the contrary.
To plot a matrix as an image you just need to call two functions:
image(myMatrix)
colormap(jet)
The colormap function defines the colour pattern used to render the image. The image you posted is using the "jet" colormap.
And to show the colour scale beside the image use the colorbar function.
I was trying use the code shown below to plot in such a way that each iso-surface will be different in color and there will be a color bar at the right. I made a ss(k) color matrix for different colors. Number of iso-surfaces is 10 but I have only 8 colors. That's why I wrote ss(9)='r' and ss(10)='r'.
I need a solution to plot the iso-surface with different color and bar at the right side.
ss=['y','m','c','r','g','b','w','k','r','r']
k=1;
for i=.1:.1:1
p=patch(isosurface(x,y,z,v,i));
isonormals(x,y,z,v,p)
hold on;
set(p,'FaceColor',ss(k),'EdgeColor','none');
daspect([1,1,1])
view(3); axis tight
camlight
lighting gouraud
k=k+1;
end
Another possibility is to draw the patches with direct color-mapping (by setting the property 'CDataMapping'='direct'), while assigning the 'CData' of each patch to an index in the colormap of your choice. This is in fact recommended for maximum graphics performance.
Consider the following example:
%# volumetric data, and iso-levels we want to visualize
[x,y,z,v] = flow(25);
isovalues = linspace(-2.5,1.5,6);
num = numel(isovalues);
%# plot isosurfaces at each level, using direct color mapping
figure('Renderer','opengl')
p = zeros(num,1);
for i=1:num
p(i) = patch( isosurface(x,y,z,v,isovalues(i)) );
isonormals(x,y,z,v,p(i))
set(p(i), 'CData',i);
end
set(p, 'CDataMapping','direct', 'FaceColor','flat', 'EdgeColor','none')
%# define the colormap
clr = hsv(num);
colormap(clr)
%# legend of the isolevels
%#legend(p, num2str(isovalues(:)), ...
%# 'Location','North', 'Orientation','horizontal')
%# fix the colorbar to show iso-levels and their corresponding color
caxis([0 num])
colorbar('YTick',(1:num)-0.5, 'YTickLabel',num2str(isovalues(:)))
%# tweak the plot and view
box on; grid on; axis tight; daspect([1 1 1])
view(3); camproj perspective
camlight; lighting gouraud; alpha(0.75);
rotate3d on
I also included (commented) code to display the legend, but I found it to be redundant, and a colorbar looks nicer.
Matlab usually plots different iso-surfaces in different colors automatically, so you don't need to care about that. What kind of bar do you need? A colorbar or a legend? Either way, it is just to use the colorbar or legend function..
%Create some nice data
[x y z] = meshgrid(1:5,1:5,1:5);
v = ones(5,5,5);
for i=1:5
v(:,:,i)=i;
end
v(1:5,3:5,2)=1
v(1:5,4:5,3)=2
%Plot data
for i=1:5
isosurface(x,y,z,v,i)
end
%Add legend and/or colorbar
legend('one','Two','Three','Four')
colorbar
Since the color bar encodes value->color, it is impossible to do what you ask for, unless there is no intersection in z-values between all pairs of surfaces. So the solution below assumes this is the case. If this is not the case, you can still achieve it by adding a constant value to each surface, so to separate the surfaces along the z axis, and eliminate any intersection.
The solution is based on constructing a colormap matrix of piecewise constant values, distributed similarly to the z values of your surfaces. So for example, if you have 3 surfaces, the first has z values between 1 and 10, the 2nd between 11 and 30, and the 3rd between 31 and 60, you should do something like this (I plot in 2D for simplicity)
r = [1 0 0];
g = [0 1 0];
b = [0 0 1];
cmap = [r(ones(10,1),:); g(ones(20,1),:); b(ones(30,1),:)];
z1 = 1:10;
z2 = 11:30;
z3 = 31:60;
figure; hold on
plot(z1,'color',r)
plot(z2,'color',g)
plot(z3,'color',b)
colorbar
colormap(cmap)
More complex colormaps (i.e, more colors) can be constructed with different mixtures of red, green, and blue (http://www.mathworks.com/help/techdoc/ref/colorspec.html)
I want to have each subplot share the same colorbar scale. I know caxis works for integers greater than 1, but there appears to be a problem using caxis with values such as 0.001.
x = 0:1:10;
y = 0:1:10;
z1 = .1:-.01:0;
z2 = .01:-.001:0;
figure;
subplot(1,2,1);
scatter(x,y,10,z1); colorbar;
subplot(1,2,2);
scatter(x,y,10,z2); colorbar;
Now I want to have the scatter subplots to have a common colorbar scale. I tried to use caxis, however I do not get the desired results. The left axis does not scale correctly, as they are all brown. How can this be corrected?
ca = [0 .01];
figure;
subplot(1,2,1);
scatter(x,y,10,z1); caxis(ca); colorbar;
subplot(1,2,2);
scatter(x,y,10,z2); caxis(ca); colorbar;
What you're seeing is the correct behaviour of caxis. When you set caxis([0 0.01]), all values greater than 0.01 are assigned the colour red (or brown, whatever you call it). In z1, all except the last point are greater than 0.01 and so they're all marked in red. If you tried caxis([0 0.1]), you'll see that the plot on the right is all blue.The dynamic range of your two subplots are an order of magnitude apart and so, you won't be able to represent both adequately with the same caxis limits.
Have you tried using a logarithmic color scale? Try the following:
subplot(1,2,1);
scatter(x,y,10,log10(z1)); colorbar;
caxis([-3 -1])
subplot(1,2,2);
scatter(x,y,10,log10(z2)); colorbar;
caxis([-3 -1])
Does the above plot look better?