如何为 patchcollection 设置 edgecolor 的颜色限制属性（python、matplotlib）

Question

I am plotting volumetric distributions with x, y and z axis (particle size, particle shape, volume (%) (z-axis as colour scale). Upon exporting the figure as svg, white space appears between the plotted rectangles. I therefore tried setting the edgecolor of the patchcollection. This works, however, the edgecolors have different clim and therefore the color of the edges differs from the patches themselves (see example figure). Code for setting the patchcollection:

p = PatchCollection(rects,cmap=matplotlib.cm.viridis)
colors = curem # colour of rectangles based on volume of the size-shape bins of curem
p.set_array(np.array(colors)) 
p.set_edgecolor(matplotlib.cm.viridis(np.array(colors))) 
p.set_clim([0, math.ceil(np.max(ems[ii]))]) # set maximum to max Rsqclass rounded up to next 1/5th
axs[zz].add_collection(p) # add all the rectangles to the figure

So how do I go about setting the color limits for the edges? Thanks in advance, Hans

Answer 1

After trying out several of Diziet Asahi's proposed solutions, I found that for this specific case, the following works:

p.set_edgecolor('face') # edgecolor equal to facecolor p.set_linewidth(0.5)

The edgecolor is now equal to the facecolor. A small linewidth (eg the suggested 0.000000000001) does not work. White lines still appear when the svg is viewed in microsoft internet explorer or inkscape. A linewidth of 0.5 gets rid of the wite space. However, it should be noted that the required linewidth depends on the level of zoom. Eg, at 400% zoom a linewidth of 0.1 is sufficient. At 30% zoom a linewidth of 0.5 is still insufficient.

One further note: the above solution is specific to svg vector graphics. When stored as .pdf, the solution that Diziet linked to actually does work (set linewidth to an infinitesimally small value).

Answer 2

There seem to be a general problem with showing undesired linestrokes with vector backends, as per this issue on matplotlib's github

A proposed temporary fix is to use very small, but non-zero linewidths:

either pass linewidths=0.000000000001 to the constructor

p = PatchCollection(rects,cmap=matplotlib.cm.viridis, linewidths=0.000000000001)

or use

p.set_linewidth(0.000000000001)