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I need to control the transparency of the markers in the figure produced with the scatterhist command in MATLAB.
The following post is helpful in handling the color of the histograms: Controlling scatterhist bar colors.
How can the transparency of the markers be modified?
How can I add a contour plot on top of the markers?
tl;dr:
In MATLAB R2019a,
scatterhist() can do contours but it is difficult (yet possible) to add marker transparency, and
scatterhistogram() can easily do transparency but contours are difficult.
See the third option below using alpha(), scatter(), and histogram() which builds this from scratch.
% MATLAB R2019a
n = 250; % Number of Points
X = exprnd(3,n,1);
Y = gamrnd(9,1/3,n,1);
Using scatterhistogram():
You can adjust the marker transparency with the MarkerAlpha Property.
T = table(X,Y);
figure
s = scatterhistogram(T,'X','Y',...
'HistogramDisplayStyle','smooth',...
'LineStyle','-')
s.MarkerAlpha = 0.5; % adjust transparency
The documentation demonstrates variations of this technique.
Notice that scatterhistogram() cannot be used with hold on either before or after, which prevents using this solution from MATLAB Central.
% This will give an error in R2019a
figure
s = scatterhistogram(T,'X','Y','HistogramDisplayStyle','smooth','LineStyle','-')
hold on
[m,c] = hist3([X', Y']); % [m,c] = hist3([X(:), Y(:)]);
contour(c{1},c{2},m)
Using scatterhist():
If you name s = scatterhist(X,Y), then s(1) is the scatter plot, s(2) & s(3) are the histograms. This allows you to change properties. Notice that s(1).Children.MarkerFaceColor = 'b' works fine but there is no MarkerAlpha or MarkerFaceAlpha property (you'll get an error telling you so).
But, contours are possible. I think transparency is possible to based on this comment from #Dev-iL, but I haven't figured it out yet.
figure
s = scatterhist(X,Y,'Direction','out')
s(1).Children.Marker = '.'
hold on
[m,c] = hist3([X(:), Y(:)]);
ch = contour(c{1},c{2},m)
Build it from scratch:
Obviously the entire thing can be manually constructed from scratch (but that's not appealing).
Using the alpha() command gets it done.
figure1 = figure;
% Create axes
axes1 = axes('Tag','scatter','Parent',figure1,...
'Position',[0.35 0.35 0.55 0.55]);
hold(axes1,'on');
% Create plot
s = scatter(X,Y,'Parent',axes1,'MarkerFaceColor','r','Marker','o');
ylabel('Y');
xlabel('X');
box(axes1,'on');
% Create axes
axes2 = axes('Tag','yhist','Parent',figure1,...
'Position',[0.0325806451612903 0.35 0.217016129032258 0.55]);
axis off
hold(axes2,'on');
% Create histogram
hx = histogram(X,'Parent',axes2,'FaceAlpha',1,'FaceColor','r',...
'Normalization','pdf',...
'BinMethod','auto');
view(axes2,[270 90]);
box(axes2,'on');
% Create axes
axes3 = axes('Tag','xhist','Parent',figure1,...
'Position',[0.35 0.0493865030674847 0.55 0.186679572132827]);
axis off
hold(axes3,'on');
% Create histogram
hy = histogram(Y,'Parent',axes3,'FaceAlpha',1,'FaceColor','r',...
'Normalization','pdf',...
'BinMethod','auto');
box(axes3,'on');
axis(axes3,'ij');
[m,c] = hist3([X(:), Y(:)]);
contour(axes1,c{1},c{2},m)
alphaVal = 0.3;
alpha(s,0.5) % Set Transparency
alpha(hx,0.5)
alpha(hy,0.5)
References:
1. Access Property Values in MATLAB
2. Plot markers transparency and color gradient
For Matlab versions prior to 2018, scatterhistogram isn't available. And so, I found an alternative easy way to accomplish that markers have transparency:
figure
scatterhist(X,Y,'Kernel','on'); hold on
hdl = get(gca,'children');
set(hdl,'MarkerEdgeColor','none')
scatter(hdl.XData,hdl.YData,50,'MarkerFaceColor','r',...
'MarkerEdgeColor','none','MarkerFaceAlpha',0.2)
This works nicely.
I have a problem with saving a Matlab figure as ".svg" and subsequently opening it in Inkscape. More precisely, I need two subplots to be a specific height, i.e. 6cm. This can be done in Matlab by setting the "Position" property (and setting the units to "centimeters"). This all works as expected and I then export the figure as ".svg"
The problem is that when I import the figure to Inkscape the axes length is close to the value I set but not correct. I.e. I set it to 6 cm and it is 6.28 in Inkscape. It is not much of an error, but it completely defeats the purpose of defining it in the first place. Any ideas?
I tried exporting the figure in several different ways but the result is always the same.
figure('name','representative plasticity figure');
set(gcf,'Color','w','units','centimeters','position',...
[0 0 8.6 8.4],'PaperPositionMode','auto');
s1=subplot(2,1,1)
img = imagesc(magic(8)); hold on;
set(gca, 'TickDir','out','FontSize',8.5,'LineWidth',0.59,'TickLength'...
,[0.03 0.00001]);
c1 = colorbar; c1.Box = 'off';c1.TickDirection = 'out'; c1.FontSize = 8.5;
ax1 = gca; ax1.Units = 'Centimeters';ax1.Position(3:4) = [3.427, 1.59];
box off; % THIS IS THE SIZE I NEED BUT WHICH ISN'T PRINTED CORRECTLY
c1.Label.String = '[whatever]';
subplot(2,1,2)
p1=plot(randi(5,5),'r','LineWidth',0.64); hold on;
box off; set(gca, 'TickDir','out','TickLength',...
[0.03 0.00001],'FontSize',8.5,'LineWidth',0.64);% legend('pre','post');
legend('boxoff');
ax2 = gca;ax2.Units = 'Centimeters';ax2.Position(3:4) = ax1.Position(3:4);
xlabel ('whatever' ); ylabel('whatever');
print myplot -dsvg
The size of the figure should be [3.427, 1.59] in cm. And it is so in the resulting matlab figure, however, in Inkscape it is more like 3.6 and 1.7.
I read a lot of answers here, but for some reason my animation still doesn't work as expected.
The axis range should vary from frame to frame. The 'Hurricane Center' caption should remain in the center all the time, but the captions from the previous frames must be erased. Also, I'm afraid that some of the data from previous parts remain.
I used hold on and draw now but it still happens.
The animation can be seen here:
Code:
v = VideoWriter('test_video.avi');
v.FrameRate = 4;
v.open()
hold on
for i=1:length(relevant(1,1,:))
if isempty(relevant) == 0
title('Lightning around Hurricane Jerry')
grid on
ylim([Interp_Jerry(i,2)-Radius Interp_Jerry(i,2)+Radius])
xlim([Interp_Jerry(i,3)-Radius Interp_Jerry(i,3)+Radius])
ylabel('latitude')
xlabel('longitude')
text(Interp_Jerry(i,3),Interp_Jerry(i,2),txt1);
scatter(relevant(:,3,i),relevant(:,2,i),'.');
drawnow
pause(0.1);
v.writeVideo(getframe(fig));
end
end
v.close()
The best of the two worlds:
v = VideoWriter('test_video.avi');
v.FrameRate = 4;
v.open()
hold on;
for i=1:length(relevant(1,1,:))
if ~isempty(relevant) % Corrected
if i == 1
% Prepare first plot and save handles of graphical objects
ht = text(Interp_Jerry(i,3),Interp_Jerry(i,2),txt1);
hold on;
hs = scatter(relevant(:,3,i),relevant(:,2,i),'.');
ylabel('latitude')
xlabel('longitude')
title('Lightning around Hurricane Jerry')
grid on
else
% Update graphical objects
set(ht, 'position', [Interp_Jerry(i,3), Interp_Jerry(i,2)]);
set(hs, 'XData', relevant(:,3,i) , 'YData' , relevant(:,2,i));
end
ylim([Interp_Jerry(i,2)-Radius Interp_Jerry(i,2)+Radius])
xlim([Interp_Jerry(i,3)-Radius Interp_Jerry(i,3)+Radius])
drawnow
pause(0.1);
v.writeVideo(getframe(fig));
end
end
v.close()
Instead of writing the text every time, just modify its position in the loop. Create a text object out side of the loop
t = text(position1, position2, txt);
in the loop change the position and if necessary the text
set(t, 'position', [new_position1, new_position2]);
If you don't want the previous data to remain, then you shouldn't use hold on... I think you should revise your code as follows:
v = VideoWriter('test_video.avi');
v.FrameRate = 4;
v.open();
fg = figure();
% Do not hold on, so that data is not retained frame-to-frame
for i=1:length(relevant(1,1,:))
% You don't need to test if 'relevant' is empty, since you're looping to its length!
% New plot
scatter(relevant(:,3,i),relevant(:,2,i),'.');
% Customise plot (labels / axes / text / ...)
title('Lightning around Hurricane Jerry')
ylabel('latitude')
xlabel('longitude')
ylim([Interp_Jerry(i,2)-Radius Interp_Jerry(i,2)+Radius]);
xlim([Interp_Jerry(i,3)-Radius Interp_Jerry(i,3)+Radius]);
text(Interp_Jerry(i,3),Interp_Jerry(i,2),txt1);
grid on;
drawnow;
% You don't need to pause whilst plotting, you already set the video framerate.
% pause(0.1);
v.writeVideo(getframe(fg));
end
v.close()
I have the following image derived from imagesc(some matrix whose entries correspond to those colors). The Cyan and the Yellow both mean different things. I would like to either:
Add a legend where I can fill in what each color means
Segregate parts of the X-axis to where I can type "cyan" on the x region below the cyan part, and "yellow" on the x region below the yellow part.
Either or would be fine, and which ever one is easier would be appropriate for me.
CYAN YELLOW
Do you want something like this? It's very basic haha.
clc
clear
close all
%// Dummy array
A = repmat([0 0 0 1 1 1],6,1);
imagesc(A)
hold on
%// Dummy data to add legend
scatter(0,0,1,'b','filled')
scatter(0,0,1,'r','filled')
axis off
colorbar
%// Get axis coordinates (x first and then y)
ax = axis;
%// Add text. You can easily adjust the x-offset depending on how many colors you have.
text(ax(2)/4+ax(1),ax(4)+.2,'Blue','Color','b','FontSize',20,'HorizontalAlignment','Center')
text(3*ax(2)/4+.2,ax(4)+.2,'Red','Color','r','FontSize',20,'HorizontalAlignment','Center')
%// Add legend
legend({'Blue';'Red'})
Output:
Here's another option, which happens to be matlab-hg2 friendly:
%% // Initialization
clear variables; close all force; clc;
%% // Generate some data
fakeData = magic(3)-0.5;
fakeData_horz = fakeData(:)'; %//'
fakeNames = cellstr(strcat('color',num2str((1:9)'))); %//'
fakeNameMapping = fakeNames(randperm(numel(fakeData)));
%% // Create figure
hFig = figure('Position',[680,488,758,610],'Resize','off');
%% // Top left example
cLims = [0 numel(fakeData)+1];
hSp = subplot(2,2,1);
imagesc(fakeData); axis image; set(hSp,'XTick',[],'YTick',[]);
colorbar; caxis(cLims);
[XX,YY] = meshgrid(1:size(fakeData,1),1:size(fakeData,2));
text(XX(:),YY(:),fakeNameMapping,'HorizontalAlignment','center');
%% // Bottom example
hSp = subplot(2,2,3:4);
cLims = [0 numel(fakeData)+1]; %Not required here since unchanged
imagesc(fakeData_horz); axis image; set(hSp,'XTick',[],'YTick',[]);
colorbar; caxis(cLims);
drawnow; %// This command will allow the annotations to be positioned properly
for ind1=1:numel(fakeData_horz)
newPos = [hSp.Position(1)+hSp.Position(3)/numel(fakeData_horz) * (ind1-1),...
hSp.Position(2)*1.6,... %1.6 is chosen for the demo
hSp.Position(3)/numel(fakeData_horz),...
0.05]; % 0.05 is chosen for the demo; play around with it
h= annotation('textbox',newPos,'String',fakeNameMapping{ind1},...
'LineStyle','none','HorizontalAlignment','center');
end
%% // Top right example
hSp = subplot(2,2,2);
cLims = [0 numel(fakeData)]; %// cLims is a bit different here!
imagesc(fakeData); axis image; set(hSp,'XTick',[],'YTick',[]);
caxis(hSp,cLims); colormap(hSp,parula(numel(fakeData)));
cb = colorbar; %// This time we need a handle to the colorbar
cb.Ticks = (hSp.CLim(1):hSp.CLim(2))+0.5; %// Set the tick positions
cb.TickLabels = fakeNames; %// Set the tick strings
Which results in:
Note: unless using a more intelligent text positioning computation, the figure's size should not be changed after it was plotted (in the 2nd example), because then the text no longer remains where it should be.
Edit: added another option where only the colorbar is labeled.
This issue is only for unix matlabs, windows users won't be able to reproduce it.
I am having trouble while trying to create datatips in which are on top of the y axis label. The following picture illustrate the issue:
As you can see, the datatips created close to the ylabel will get bottom to the ylabel text, while the desire effect is the opposite: the datatip to be on top of the axis label.
I generated the plot with the following (not so minimal) code, which is available bellow. You may remove the lines commented with % may be removed, or even just put a datatip on −78 instead of a loop in order to achieve a faster testing script, but I leave this code if someone one day wants it to create custom datatips (in this case, consider seeing also http://undocumentedmatlab.com/blog/controlling-plot-data-tips/):
gradientStep = 1e-1;
x=-100:gradientStep:100; xSize=numel(x);
y=x.^3-x.^2;
figH=figure(42);
lineH=plot(x,y);
ylabel('YLabel (YUnits)','FontSize',16)
xlabel('XLabel (XUnits)','FontSize',16)
dcH=datacursormode(figH);
nTips = 20; % May change the loop for a datatip at x=-78.
for pos = round(linspace(2,xSize,nTips))
datatipH=dcH.createDatatip(lineH,...
struct('Position',[x(pos) y(pos)]));
orientation = 'top-left';
if pos>1
tipText{1} = 'The grandient here is: ';
tipText{2} = ['\Deltax:',sprintf('%d',x(pos)-x(pos-1)),' XUnits'];
tipText{3} = ['\Deltay:',sprintf('%d',y(pos)-y(pos-1)),' YUnits'];
else
tipText = 'Cannot calculate gradient here.';
end
bkgColor = [1 1 .5]; % May be removed.
fontSize = 12; % May be removed.
set(datatipH,'StringFcn',(#(~,~) tipText),'Orientation',...
orientation,'backGroundColor',bkgColor,'FontSize',...
fontSize,'Draggable','on'); % Only set text and orientation needed.
datatipTextBoxH=get(datatipH,'TextBoxHandle'); % May be removed.
uistack(datatipH,'top'); % Unfortunately makes no effect, since the ylabel handles is not at the axes children list
datatipTextBoxH=get(datatipH,'TextBoxHandle');
set(datatipTextBoxH,'HorizontalAlignment','left',...
'VerticalAlignment','top','Margin',0.02,'Interpreter',...
'tex','FontName','Courier','FontSize',fontSize); % May be removed.
end
uistack(get(gca,'YLabel'),'bottom') % Also makes no effect, for the same reason.
I have tried:
uistack all datatips to top,
uistack the label to bottom (both of them don't work because the ylabel handle is not in the axes children handles).
Update: After implementing the #horchler' solution, a new issue appeared: when zooming and panning the axes, the axes label would also move. I've found a small fix for that, I changed the following aspects:
Set datatip z-value to 1, so that it will always be higher than ylabel axis z.
Recreating the ylabel afterwards a pan or zoom movement occurs. For this, I implemented localAxisUpdate function that get the old ylabel properties, replace it by a new one, and them reset all settable properties but the ylabel position. For this I used this reference
The resulting code is as follows:
function test
gradientStep = 1e-1;
x=-100:gradientStep:100; xSize=numel(x);
y=x.^3-x.^2;
figH=figure(42);
lineH=plot(x,y);
ylabel('YLabel (YUnits)','FontSize',16)
xlabel('XLabel (XUnits)','FontSize',16)
dcH=datacursormode(figH);
%nTips = 20;
%for pos = round(linspace(2,xSize,nTips))
pos = find(x>-78,1);
datatipH=dcH.createDatatip(lineH,...
struct('Position',[x(pos) y(pos) 1]));
orientation = 'top-left';
if pos>1
tipText{1} = 'The grandient here is: ';
tipText{2} = ['\Deltax:',sprintf('%d',x(pos)-x(pos-1)),' XUnits'];
tipText{3} = ['\Deltay:',sprintf('%d',y(pos)-y(pos-1)),' YUnits'];
else
tipText = 'Cannot calculate gradient here.';
end
bkgColor = [1 1 .5]; % Light Yellow
fontSize = 12;
set(datatipH,'StringFcn',(#(~,~) tipText),'Orientation',...
orientation,'backGroundColor',bkgColor,'FontSize',...
fontSize,'Draggable','on');
datatipTextBoxH=get(datatipH,'TextBoxHandle');
datatipTextBoxH=get(datatipH,'TextBoxHandle');
set(datatipTextBoxH,'HorizontalAlignment','left',...
'VerticalAlignment','top','Margin',0.02,'Interpreter',...
%end
% Set changes due to zoom and pan to also use adaptativeDateTicks:
set(zoom(figH),'ActionPostCallback',...
#(~,~) localAxisUpdate(gca));
set(pan(figH),'ActionPostCallback',...
#(~,~) localAxisUpdate(gca));
end
function localAxisUpdate(aH)
% Fix axis label on top of datatip:
ylh = get(aH,'YLabel');
% Get original YLabel properties
ylstruct = get(ylh);
% Get settable fields:
yfieldnames=fieldnames(rmfield(set(ylh),'Position'))';
% Remove old label:
delete(ylh)
% Create new one:
ylh = ylabel(aH,'Dummy');
% Send it bottom:
ylpos = get(ylh,'Position');
set(ylh, 'Position', [ylpos(1:2) 0]);
% Reset new ylabel to old values:
for field=yfieldnames
field = field{1};
set(ylh,field,ylstruct.(field));
end
end
This approach creates an unwanted effect, which is the ylabel will move across the figure until the mouse button is released. How can I remove this unwanted effect ?
I think the solution may be more or less as it was done in undocummented matlab solution for updating axes ticks, but now I would need the listener to the ylabel postset property. Does anyone knows how to do that? If you are a windows user, you can also try to help, all I need is to reset the position of the ylabel after a change (pan, zoom or whatever) is made on the figure.
How about explicitly setting the z-position of the y-label via it's handle? If I put this after your loop it seems to work in R2012b:
ylh = get(gca,'Ylabel')
ylpos = get(ylh,'Position');
set(ylh,'Position',[ylpos(1:2) 0]);
If I adjust the z-position I can get the y-label to pop up and even interleave between the datatips. I'm not completely sure if this is a bug or a feature, but sometimes there are workarounds to rendering issues that involve tweaking the position of an element slightly to get Matlab to recalculate and redraw the figure.
A workaround that uses both linkaxes, so useful when zooming/panning multiple plots, and the visibilty of plots.
create an axes (hax_1) with the function to be plotted, without the datatips
create an axes (hax_2) with the function to be plotted AND the datatips but without the axes labels
set hax_2 visibility to 'off' (this will plot the datatips above the first axes labels)
link the 2 axes with linkaxes([hax_1 hax_2],'xy'); (zooming and panning on one of the axes will modify on the fly the second axes)
This gives with your first code (not the edited one):
gradientStep = 1e-1;
x=-100:gradientStep:100; xSize=numel(x);
y=x.^3-x.^2;
figH=figure(42);
plot(x,y);
ylabel('YLabel (YUnits)','FontSize',16)
xlabel('XLabel (XUnits)','FontSize',16)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% modification starts
hax_1 = gca;
hax_2 = axes('Position', get(hax_1,'Position'));
lineH = plot(x,y);
linkaxes([hax_1 hax_2],'xy');
set(hax_2,'Visible', 'off');
% modification ends
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dcH=datacursormode(figH);
nTips = 20; % May change the loop for a datatip at x=-78.
for pos = round(linspace(2,xSize,nTips))
datatipH=dcH.createDatatip(lineH,struct('Position',[x(pos) y(pos)]));
orientation = 'top-left';
if pos>1
tipText{1} = 'The grandient here is: ';
tipText{2} = ['\Deltax:',sprintf('%d',x(pos)-x(pos-1)),' XUnits'];
tipText{3} = ['\Deltay:',sprintf('%d',y(pos)-y(pos-1)),' YUnits'];
else
tipText = 'Cannot calculate gradient here.';
end
bkgColor = [1 1 .5]; % May be removed.
fontSize = 12; % May be removed.
set(datatipH,'StringFcn',(#(~,~) tipText),'Orientation',orientation,'backGroundColor',bkgColor,'FontSize',fontSize,'Draggable','on'); % Only set text and orientation needed.
datatipTextBoxH=get(datatipH,'TextBoxHandle');
set(datatipTextBoxH,'HorizontalAlignment','left','VerticalAlignment','top','Margin',0.02,'Interpreter','tex','FontName','Courier','FontSize',fontSize); % May be removed.
end
I am on OSX 10.8.4, R2012b, and had the same issue as yours. Here, the proposed solution plots datatips above the axis labels and allow zooming/panning without making use of undocumented features of matlab.