How can I make the plot transparent in a gscattter?

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I have a huge amount of data which is grouped and displayed in a plot with the help of gscatter. In order to make it more visible I'd like to change the transparency of each point. But functions such as MakeFaceAlpha etc did not work at all.

Accepted Answer

Adam Danz
Adam Danz on 4 Aug 2020
Edited: Adam Danz on 27 Aug 2020
Setting transparency of markers with gscatter is not possible as of r2020a.
Update: See Yair's method of setting gscatter marker transparency using undocumented features.
Workarounds
You could use scatter() which does support transparency. Here's one way to translate a gscatter syntax to scatter syntax using arrayfun.
% gscatter syntax
gscatter(x,y,g)
% scatter syntax
cla()
hold on % important
uniqueGroups = unique(group);
h = arrayfun(@(g)scatter(x(group==g), y(group==g), 'filled'), uniqueGroups);
set(h, 'MarkerFaceAlpha', 0.6) % set transparency level
% scatter syntax specifying color, marker, and size
colors = 'rb';
markers = '^v';
uniqueGroups = unique(group);
cla()
hold on % important
h = arrayfun(@(g)scatter(x(group==g), y(group==g), ...
100, colors(g), 'filled', 'Marker', markers(g)), uniqueGroups);
set(h, 'MarkerFaceAlpha', 0.4, 'MarkerEdgeColor', 'k', 'MarkerEdgeAlpha', .2) % set transparency level
Alternatively, you could use gscatter without filled markers.
h = gscatter(x,y,g,colors,'os',10);
set(h,'LineWidth',1)
Why transparency in gscatter doesn't work
The scatter function creates scatter objects. Scatter objects have MarkerFaceAlpha and MarkerEdgeAlpha properties that allow you to set transparency levels.
The gscatter function creates line objects. Line objects do not have these properties. Furthermore, an undocumented method of adding transparancy to some graphics objects by adding a 4th element (0:1) to the RGB color definition does not work with gscatter.
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More Answers (1)

Yair Altman
Yair Altman on 27 Aug 2020
Edited: Yair Altman on 5 Oct 2022
Nice answer Adam, but not exactly accurate if you are willing to use some undocumented features...
The underlying objects in a gscatter are simple line objects, whose markers can indeed be made to be transparent: http://undocumentedmatlab.com/articles/plot-markers-transparency-and-color-gradient
The trick is to realize that only the markers' Face can be made transparent, not the markers' Edge. By default, gscatter uses empty marker Face and non-empty Edge with a '.' marker; we can change this to a 'o' marker with no edge and a non-empty Face.
Here's a simple usage example:
load carsmall
h = gscatter(Displacement, Horsepower, Model_Year);
set(h(1), 'Marker','o', 'MarkerSize',5, 'MarkerEdgeColor','none', 'MarkerFaceColor','r');
drawnow
set(h(1).MarkerHandle, 'FaceColorType','truecoloralpha', 'FaceColorData',uint8([200;0;0;50]));
% ...and similarly for the other handles h(2),h(3),...
drawnow
  7 Comments
Gernot Reichl
Gernot Reichl on 16 Nov 2022 at 10:41
Edited: Gernot Reichl on 16 Nov 2022 at 10:41
@Yair Altman Thank you very much for your answers and your great work!

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