Semi-transparent markers on log-log scatter plot

Question

I have been trying to get semi-transparent circle-shape markers on a log-log scatter plot. MATLAB's own scatter plot function doesn't produce semi-transparent markers (see comments below), so I am using this wonderful tool scatter_patches from Central File Exchange and it works very well:

However, I am having issues adapting this code for a log-log scatter plot. In order to obtain a log-log scatter plot with this program, I need to fix two things:

1 . Change the axes to log scale. This can be achieved by adding following after line 61:

set(cax, 'XScale', 'log'); 
set(cax, 'YScale', 'log');

This produces correct log scale and grid points.

2 . However, after I fixed 1., the size of the markers was not uniform in my plot. On a log plot, the lower-value regions of the axes are zoomed-in. In the scatter_patches plot, the markers at the lower side of axes are bigger while they are smaller towards the higher-value side of axes. So, the marker size is not the same on the entire plot. I tried using log10(cSize) instead of cSize on lines 221-222, but this only slimmed the difference between the largest and smallest marker sizes. It didn't yield the same size markers on the plot.

If anyone has an idea of what I might be missing here, please share.

Any help would be greatly appreciated.

Have you tried to use Matlab's scatter plot with set(hadle_to_scatterplot,'MarkerFaceColor','None')? It seems like scatter_patches create a circle instead of marker. — Crowley
I have tried it. Setting 'MarkerFaceColor' to 'None' is equivalent to setting transparency to 100%. However, I want to control the transparency. If a property like 'MarkerFaceAlphaValue' existed, then I could have set transparency to arbitrary values. But such a property doesn't exist. The scatter_patches uses patches in place of markers; so a FaceAlphaValue can be set. This program also allows creation of other shapes, not just circles. The program works very well on linear plots. It is the log plot where some changes are required. — r2d2
I think that this article will interest you. Have you try to add an exp()here: set(patchObjects(i), 'XData', cSize * sin(patchSpec) / ptsPerXUnit + xs(i)); set(patchObjects(i), 'YData', cSize * cos(patchSpec) / ptsPerYUnit + ys(i));like set(patchObjects(i), 'XData', cSize * exp(sin(patchSpec))/ ptsPerXUnit + xs(i)); But i didn't tried ! — obchardon
Ups: more like this: set(patchObjects(i), 'XData', exp(cSize * sin(patchSpec)/ ptsPerXUnit + xs(i))); and the same for YData — obchardon

Robert Seifert Robert Seifert · Accepted Answer · 2016-04-07T12:46:25

Since Matlab R2014b things got really easy. No additional functions from file exchange are required, just some undocumented features. The basic idea is to get the hidden handle of the markers and apply a value < 1 for the last value in the EdgeColorData to achieve the desired transparency.

Here we go:

%// example data
x = linspace(0,3*pi,200);
y = cos(x) + rand(1,200);

%// plot scatter, get handle
h = scatter(x,y); 
drawnow; %// important

%// get marker handle
hMarkers = h.MarkerHandle; 

%// get current edge and face color
edgeColor = hMarkers.EdgeColorData
faceColor = hMarkers.FaceColorData

%// set face color to the same as edge color
faceColor = edgeColor;

%// opacity
opa = 0.3;

%// set marker edge and face color
hMarkers.EdgeColorData = uint8( [edgeColor(1:3); 255*opa] ); 
hMarkers.FaceColorData = uint8( [faceColor(1:3); 255*opa] );

Semi-transparent markers on log-log scatter plot

3 Answers