I am trying to plot a matrix where each element is in one out of two states. (ising model..)
Now, I would like to have one state colored and the other one white. That works using
[i,j] = find(S);
figure(gcf);
plothandle = scatter(i,j);
axis([0 nNodes+1 0 nNodes+1]);
when S holds the Spins and one state is equal to 0. (find returns a matrix of only non-zero elements)
To have a useful plot, the sizes of the markers should be 1x1 in RELATIVE coordinates. So if the whole matrix S would be in a state non-zero, everything would be colored.
However, it seems like Matlab only allows MarkerSizes in points or inches. How could I solve this?
One idea I had was, that I find out the point-size of the axes and then can easily calculate how big my markers should be. Then I would have to create a callback function if I want to zoom in and so on. Also, I have not yet found a way (without the image acq. toolbox) to find out the absolute size of my axes.
To clarify what I want: How could I plot a chessboard using a matrix with 1 for black and 0 for white fields?
For displaying data of this sort I generally prefer IMAGE or IMAGESC to PCOLOR since PCOLOR won't display the last row and column of the matrix when using faceted shading (the default). Also, IMAGE and IMAGESC flip the y axis so the image more intuitively matches what you think of when looking at a matrix (i.e. rows start from 1 at the top). You can visualize your matrix like this:
S = round(rand(20)); %# Sample 20-by-20 matrix of ones and zeroes
imagesc(S); %# Plot the image
colormap([1 1 1; 0 0 0]); %# Set the colormap to show white (zero elements) and
%# black (non-zero elements)
And here's a sample image:
Just as a suggestion, you can try using pcolor instead of `scatter' Example:
pcolor(hadamard(20))
colormap(gray(2))
axis ij
axis square
Related
I am trying to write a script to plot florescence intensity from some microscopy data as a scatter plot and threshold this data based on cells that respond greater than a certain amount in CFPMAX and plot these in green and cells that do not in red. When I try to plot this, I am unable to really assign proper colors to points and they end up being blue and red. I need each cell in the image to be assigned 4 values, (3 values for for each florescence channel and one value to determine whether or not it responded (green or red). Thus I was wondering if it was possible to assign the proper color to the 4th column of the matrix, or if I am going about this the wrong way all together. I have attached my code below.
MCHR=csvread('data1.csv');
MYFP=csvread('data2.csv');
MCFP=csvread('data3.csv');
CFPMAX=(max(MCFP))';
MCHMAX=(max(MCHR))';
YFPMAX=(max(MYFP))';
c=zeros(length(CFPMAX));
for i=1:length(c)
if CFPMAX(i)>40
c(i)='g'; %// green responders
else
c(i)='r'; %// red non-responders
end
end
MM=horzcat(MCHMAX,YFPMAX,CFPMAX,c);
scatter(MM(:,1),MM(:,2),100,MM(:,4),'filled','MarkerEdgeColor',[0 0 0])
title('Responders vs Non-Responders ')
xlabel('[TF1]') %// x-axis label
ylabel('[TF2]') %// y-axis label
As far as I can tell from the documentation, the input parameter c (assuming scatter(x,y,a,c,...)) can be one of:
A single character specifying a colour e.g. 'g' or 'r'. But just one single scalar colouring all of you points.
A single RGB triple colouring all of your points so [1,0,0] for red or [0,1,0] for green.
A three column matrix of RGB triples. This is likely what you want. I will demonstrate this to you.
A one column matrix of numbers which will colour the points according to a colormap. This one will also work for you but less explicitly. Incidentally, I would guess that this is option that MATLAB though your vector of characters was.
So in order to create the matrix of RGB triples you can modify your code to be
c=zeros(length(CFPMAX),3);
for i = 1:length(CFPMAX)
if CFPMAX(i)>40
c(i,:)=[0,1,0]; %// green responders
else
c(i,:)=[1,0,0]; %// red non-responders
end
end
However, you could actually do away with the for-loop completely in MATLAB and construct c in a vectorized approach using logical indexing:
c=zeros(length(CFPMAX),3);
c(CFPMAX > 40, 2) = 1; %// green responders
c(CFPMAX <= 40, 1) = 1; %// red responders
This is a more idiomatic way to do this in MATLAB.
I want to plot a text file with 4 columns that first column in longitude,second in latitude, third is depth and forth is amount of displacement in each point.(it's related to a fualt)
-114.903874 41.207504 1.446784 2.323745
I want a plot to show the amount of displacement in each point (like images that we plot with imagesc),unfortunately "imagesc" command doesn't work for it.
how can I plot it?
Thanks for your attention
A simple way would be to use scatter3 and assign your displacements to be the colours. Note that you have to supply a size for this to work - I'm using [] (empty matrix) which will set it to default. If your four sets of values are four vectors of the same size, then it's just something like:
scatter3(lat,lon,depth,[],displacement, 'filled')
Values in displacement will be linearly mapped to the current colormap. 'filled' gives you filled markers rather than open ones (default marker is a circle but can be changed).
You can plot each point using plot3(longitude,latitude,depth). You can color each point according to the displacement in a for loop. The easiest way to do this is create a colormap, e.g. using jet and chosing the color according to the displacement.
figure;
hold on;
cmap = jet(256);
dispRange = [min(displacement),max(displacement)];
for k=1:size(longitude,2)
c = cmap(1+round(size(cmap,1)*(displacement(k)-dispRange(1))/dispRange(2)),:);
plot3(longitude(k),latitude(k),depth(k),'o', ...
'MarkerEdgeColor',c,'MarkerFaceColor',c);
end
I am trying to plot an image of a matrix using the pcolor(). The matrix presents a field. (In my case a sea field! But it does not matter:) ). The problem is that when I plot the matrix using pcolor() the matrix is ploted mirrored.
An example:
A=[1 0 0;0 1 0;0 0 1];
If I plot the matrix, the cell (0,0) will be plotted not in the top left corner but in the bottom left corner.(Its obvious the start of the axes is (0,0) I understand that the function is working properly!) I know also the existence of the flipdim() functions to flip the matrix.
The problem is that the code becomes ugly if I use this approach.For example the cell(0,0) in the matrix will be appeared in cell(size(A,1),0) and everything becomes opposite! How can I face that problem in a more elegant way?
(The matrix to be printed as a terian for example and not mirrored)
Edit:
Solved using axis ij
In general, to change the direction of axis you can set YDir (or XDir) property from normal to reverse.
set(gca,'YDir','rev')
PCOLOR function produce axis with YDir set to normal. In opposite, IMAGESC's YDir is reverse by default.
I'm plotting two pcolors on top of each other (using the m_map algorithm m_pcolor). The reason for this is that the second pcolor has transparency in it, and so shows the pcolor underneath. The first plot consists of just ones and zeroes, and I would like it to be just black and white. I would like the second to use the colormap jet, but I can't work out how to set one colormap without changing the other. My code at the moment is:
h1 = m_pcolor(Lon', Lat', black_background);
hold on;
h = m_pcolor(Lon', Lat', input_matrix);
Thanks in advance,
Adam
For this limited application, the easiest way is probably to append a row of zeros onto the colormap, deal with scaling (the clim property) yourself so that each plot takes advantage of the appropriate part of the colormap.
cm=colormap('jet'); %# Nx3
cm = [cm; 0 0 0]; %# append black row: (N+1)x3
h1 = m_pcolor(Lon',Lat',black_background);
set(h1,'clim',[length(colormap),length(colormap)])
hold on
h2 = m_pcolor(Lon', Lat', input_matrix);
set(h2,'clim',[length(colormap)-1, length(colormap)-1])
This should get you close, but I haven't tested it since I'm not on my matlab machine.
Another option is freezeColors from the file exchange (but this may only work for different axes within the same figure window, I'm not sure about different plots in the same axes object).
I have generated a plot like
figure; hold;
axis([0 10 0 10]);
fill([ 1 1 5 5], [5 1 1 5],'b')
and now I want to have this plot as an matrix so that I can i.e. filter the blog with a gaussian. Googleing I found this thread Rasterizing Plot to Image at MATLAB Central. I tried it, but I could only get it to work for line or function plots.
Do you have any ideas?
You can use GETFRAME function. It returns movie frame structure, which is actually rasterized figure. Field cdata will contain your matrix.
F=getframe;
figure(2)
imagesc(F.cdata);
What are the desired characteristics of your target matrix ? And what sort of images do you want to rasterise ?
You see, for the only example you have given us it's almost trivial to define a matrix representing your image ...
1. figmat = ones(10,10,3) % create a 10x10 raster where each entry is a triple for RGB, setting them all to 1 colours the whole raster white
2. figmat(2:5,2:5,1:2) = 0 % sets RG components in the coloured area to 0, leaving only blue
Your matrix is a raster to start with. Now, you can use the built-in function image to visualise your matrix. Have a look at the documentation for that function. And note that my suggestion does not meet the spec for use with image() and colormap().