How can I make the plot transparent in a gscattter?

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.

Answer 1

[Adam Danz]

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.

[Adam Danz]

Note: Demo plot created with

load discrim % built-in dataset
x = ratings(:,1);
y = ratings(:,2); 
g = group;

[Mel]

Thank you very much! This helps a lot

Answer 2

[Yair Altman]

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

[Adam Danz]

Thanks, Yair! I should have known to check your blog, first!

[Sim]

I do not see any transparency with this method @Yair Altman @Adam Danz....any other example ??

[Adam Danz]

Yes, see my answer.

[Yair Altman]

@sim - simply add a call to drawnow before setting the MarkerHandle's properties, and then you'll see the transparency effect (at least in R2022b, there's no guarranty that it will continue working in future releases as well)

[Gernot Reichl]

Hi all.

I try to set the face-color property of a plot as described (in a live script ==> see attachment). But it does not work. Do you have any ideas why? Release: 2022b

x=1:10; y=10*x; hLine=plot(x,y,'o-');

drawnow;

hMarkers = hLine.MarkerHandle;

hMarkers.get;

drawnow;

hMarkers.FaceColorData = uint8(255*[1;0;0;0.3]);

hMarkers.get;

Running the live-script in command line leads to red markers with no transparency.

thank you very much in advance

[Yair Altman]

2 problems with your code:

1. you forgot to set the MarkerHandle.FaceColorType to 'truecoloralpha'
2. live scripts embedded figures do not show transparency, only standard standalone figures (i.e., run your code in a .m file, not .mlx)

[Gernot Reichl]

@Yair Altman Thank you very much for your answers and your great work!

[Joseph Mattson]

Thank you @Yair Altman for the excellent solution. One follow up to @Gernot Reichl (in 2022b anyway): Figures in .mlx scripts will show transparency if you use the "MarkerFaceAlpha" in a standard scatter plot, e.g.

scatter(x, y, 'filled','MarkerFaceAlpha',0.1);

This does not appear to be the case in line plots (which underly the gscatter). To get transparency in your grouped scatter plots in a live script, I think you'll have to use the technique highlighed by @Adam Danz and avoid gscatter altogether.