python3's adjust_text is moving text badly

Question

I have overlapping text from my script:

import matplotlib.pyplot as plt
from adjustText import adjust_text
x = [12,471,336,1300]
y = [2,5,4,11]
z = [0.1,0.2,0.3,0.4]
im = plt.scatter(x, y, c = z, cmap = "gist_rainbow", alpha = 0.5)
plt.colorbar(im)
texts = []
texts.append(plt.text(783, 7.62372448979592, 'TRL1'))
texts.append(plt.text(601, 6.05813953488372, 'CFT1'))
texts.append(plt.text(631, 4.28164556962025, 'PTR3'))
texts.append(plt.text(665, 7.68018018018018, 'STT4'))
texts.append(plt.text(607, 5.45888157894737, 'RSC9'))
texts.append(plt.text(914, 4.23497267759563, 'DOP1'))
texts.append(plt.text(612, 7.55138662316476, 'SEC8'))
texts.append(plt.text(766, 4.1264667535854, 'ATG1'))
texts.append(plt.text(681, 3.80205278592375, 'TFC3'))
plt.show()

which shows overlapping text:

however, when I add adjust_text:

import matplotlib.pyplot as plt
from adjustText import adjust_text
x = [12,471,336,1300]
y = [2,5,4,11]
z = [0.1,0.2,0.3,0.4]
im = plt.scatter(x, y, c = z, cmap = "gist_rainbow", alpha = 0.5)
plt.colorbar(im)
data = [
    (783, 7.62372448979592, 'TRL1'),
    (601, 6.05813953488372, 'CFT1'),
    (631, 4.28164556962025, 'PTR3'),
    (665, 7.68018018018018, 'STT4'),
    (607, 5.45888157894737, 'RSC9'),
    (914, 4.23497267759563, 'DOP1'),
    (612, 7.55138662316476, 'SEC8'),
    (766, 4.1264667535854, 'ATG1'),
    (681, 3.80205278592375, 'TFC3')
]

texts = [plt.text(x, y, l) for x, y, l in data]
adjust_text(texts)
plt.savefig('adjust.text.png', bbox_inches='tight', pad_inches = 0.1)

the labels are shifted to the lower left corner, making them useless, instead of just a little overlapped.

I am following clues from adjust_text(texts) as suggested by the below two links,

How to adjust text in Matplotlib scatter plot so scatter points don't overlap?

and https://adjusttext.readthedocs.io/en/latest/Examples.html

I get this:

how can I get adjust_text to fix the overlapping labels?

Answer 1

You don't show how you call adjust_text but doing it like below, works for me :

# top of the code..

adjust_text(texts)

plt.show()

And BTW, you could also simplify the way you make the texts list :

data = [
    (783, 7.62372448979592, 'TRL1'),
    (601, 6.05813953488372, 'CFT1'),
    (631, 4.28164556962025, 'PTR3'),
    (665, 7.68018018018018, 'STT4'),
    (607, 5.45888157894737, 'RSC9'),
    (914, 4.23497267759563, 'DOP1'),
    (612, 7.55138662316476, 'SEC8'),
    (766, 4.1264667535854, 'ATG1'),
    (681, 3.80205278592375, 'TFC3')
]

texts = [plt.text(x, y, l) for x, y, l in data]