scatter plot with aligned annotations at each data point

Question

I want to produce a scatter plot with dozens of points, which could potentially be very close to each other. I've tried the method of annotation from the answer to the question:

>> matplotlib scatter plot with different text at each data point

but you can see that the labels / annotations overlap when the points are close enough to each other. Is there any library or method to generate such plots with individual annotations that don't collide with each other, nor with borders of the plot?

import matplotlib.pyplot as plt

z = [0.15, 0.3, 0.45, 0.46, 0.6, 0.75]
y = [2.56422, 3.77284, 3.52623, 3.52623, 3.51468, 3.02199]
n = [58, 651, 393, "393(2)", 203, 123]

fig, ax = plt.subplots()
ax.scatter( z, y )

for i, txt in enumerate( n ):
    ax.annotate( txt, ( z[i] + .01, y[i] + .01 ) )

plt.show()

thank you for pointing me in that direction. I've tested it and it works nice! however there are some issues with longer text, the label bounding box parameters don't depend on the text length. I'll try to make them dynamic — ellockie
– ellockie, Commented Mar 24, 2015 at 14:34

Phlya · Accepted Answer · 2017-01-07 09:47:14Z

12

I have written a library adjustText which does exactly this. https://github.com/Phlya/adjustText

z = [0.15, 0.3, 0.45, 0.46, 0.6, 0.75]
y = [2.56422, 3.77284, 3.52623, 3.52623, 3.51468, 3.02199]
n = [58, 651, 393, "393(2)", 203, 123]

fig, ax = plt.subplots()
ax.scatter( z, y )
texts = []
for i, txt in enumerate( n ):
    texts.append(ax.text(z[i], y[i], txt))
adjust_text(texts)
plt.show()

answered Jan 7, 2017 at 9:47

Phlya

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