Matplotlib markers disappear when edgecolor = 'none'

python matplotlib python-2.7 markers
Mat Leonard picture Mat Leonard · Apr 4, 2012 · Viewed 48.7k times · Source

I'm trying to make a scatter plot of some PCA data. I do some pretty typical code:

plt.plot(pca[:,0], pca[:,1], '.',ms=3,  markerfacecolor = self.colors[k],
            markeredgecolor = 'none')

I want it to show just the marker face color with no outline. The problem is that the markers disappear completely when markeredgecolor = 'none'. When I set markerfacecolor='none' or to a color and remove markeredgecolor, it works like expected.

I just updated matplotlib, numpy, etc. to the newest versions, running on Python 2.7.

Thanks for your help.

Answer

Joe Kington picture Joe Kington · Apr 5, 2012

I think this is a bug that was fixed a few months ago: https://github.com/matplotlib/matplotlib/pull/598

Regardless of how large you make the markers or if you use marker='o' instead of '.', they'll be invisible if you use markeredgecolor='none'.

As a workaround, you can just set the edge colors to the same as the face colors.

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