Phlya
adjust_text weirdly changed the y_position of the points into a dense cluster.
python 3.9 Macbook Pro M2 2022 pycharm
plt.figure()
x = np.random.randn(30)
y = np.random.randn(30)
plt.scatter(x, y)
texts = [plt.text(x_pos, y_pos, f"position-{ele:.2f}") for (x_pos, y_pos, ele) in zip(x, y, x)]
a toy example to generate overlapping text
before:
after:
plt.figure()
x = np.random.randn(30)
y = np.random.randn(30)
plt.scatter(x, y)
texts = [plt.text(x_pos, y_pos, f"position-{ele:.2f}") for (x_pos, y_pos, ele) in zip(x, y, x)]
adjust_text(texts, arrowprops=dict(arrowstyle="->", color='r', lw=0.5))
no sure what went wrong. Thanks for any feedback in advance.
I am sorry, I can't reproduce this... Neither with the latest release, not with the latest version on master. I get something reasonable like this
it seems it is somehow not compatible with some packages in my conda environment. I tried the code in a base environment, where it only has a few basic packages installed, and it worked. But it kept producing the weird effect in my conda environment. my environment has the following packages
Package Version
------------------------ -----------
absl-py 1.2.0
adjustText 0.8
aiohttp 3.8.4
aiosignal 1.3.1
anndata 0.8.0
annoy 1.17.1
anyio 3.6.2
appdirs 1.4.4
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.2.2
asttokens 2.0.8
astunparse 1.6.3
async-timeout 4.0.2
attrs 22.1.0
backcall 0.2.0
beautifulsoup4 4.11.1
bhtsne 0.1.9
bioinfokit 2.1.0
biomart 0.9.2
biopython 1.81
bleach 5.0.1
bokeh 2.4.3
bravado 11.0.3
bravado-core 5.17.0
cached-property 1.5.2
cachetools 5.2.0
certifi 2022.6.15
cffi 1.15.1
charset-normalizer 2.1.1
click 8.1.3
cloudpickle 2.2.1
comtypes 1.1.14
cycler 0.11.0
Cython 0.29.32
dask 2023.2.0
datacache 1.1.5
datasets 2.9.0
debugpy 1.6.3
decorator 5.1.1
defusedxml 0.7.1
dill 0.3.6
docker-pycreds 0.4.0
entrypoints 0.4
et-xmlfile 1.1.0
etils 0.9.0
executing 1.1.1
fastjsonschema 2.16.2
filelock 3.9.0
flatbuffers 1.12
fonttools 4.36.0
fqdn 1.5.1
frozenlist 1.3.3
fsspec 2023.1.0
gast 0.4.0
gitdb 4.0.10
GitPython 3.1.31
google-auth 2.11.0
google-auth-oauthlib 0.4.6
google-pasta 0.2.0
googleapis-common-protos 1.56.4
grpcio 1.48.0
gseapy 0.14.0
gtfparse 1.2.1
h5py 3.6.0
huggingface-hub 0.12.1
idna 3.3
imbalanced-learn 0.9.1
importlib-metadata 4.12.0
importlib-resources 5.10.0
iniconfig 1.1.1
ipykernel 6.16.1
ipython 8.5.0
ipython-genutils 0.2.0
ipywidgets 8.0.2
isoduration 20.11.0
jedi 0.18.1
Jinja2 3.1.2
joblib 1.1.0
jsonpointer 2.3
jsonref 0.2
jsonschema 4.14.0
jupyter 1.0.0
jupyter_client 7.4.3
jupyter-console 6.4.4
jupyter_core 4.11.2
jupyter-server 1.21.0
jupyterlab-pygments 0.2.2
jupyterlab-widgets 3.0.3
keras 2.9.0
Keras-Preprocessing 1.1.2
kiwisolver 1.4.4
kneed 0.8.1
libclang 14.0.6
llvmlite 0.39.0
locket 1.0.0
Markdown 3.4.1
MarkupSafe 2.1.1
matplotlib 3.5.3
matplotlib-inline 0.1.6
matplotlib-venn 0.11.7
memoized-property 1.0.3
mistune 2.0.4
mock 4.0.3
monotonic 1.6
msgpack 1.0.4
multidict 6.0.4
multiprocess 0.70.14
munkres 1.1.4
natsort 8.2.0
nbclassic 0.4.5
nbclient 0.7.0
nbconvert 7.2.2
nbformat 5.7.0
ncafs 0.2
nest-asyncio 1.5.6
networkx 3.0
notebook 6.5.1
notebook_shim 0.2.0
numba 0.56.0
numpy 1.22.4
oauthlib 3.2.0
opencv-python 4.7.0.68
openpyxl 3.0.10
opt-einsum 3.3.0
packaging 21.3
pacmap 0.6.5
pandas 1.4.3
pandocfilters 1.5.0
parso 0.8.3
partd 1.3.0
pathtools 0.1.2
patsy 0.5.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.2.0
pip 22.2.2
plastid 0.6.1
pluggy 1.0.0
progressbar33 2.4
prometheus-client 0.15.0
promise 2.3
prompt-toolkit 3.0.31
protobuf 3.19.4
psutil 5.9.3
ptyprocess 0.7.0
pure-eval 0.2.2
py 1.11.0
pyarrow 11.0.0
pyasn1 0.4.8
pyasn1-modules 0.2.8
pycparser 2.21
pyEDFlib 0.1.30
pyensembl 2.0.1
Pygments 2.13.0
pynndescent 0.5.7
pyoncoprint 0.2.2
pyparsing 3.0.9
pyrsistent 0.18.1
pysam 0.20.0
pytest 7.1.3
pyts 0.12.0
pytz 2022.2.1
PyYAML 6.0
pyzmq 24.0.1
qtconsole 5.3.2
QtPy 2.2.1
requests 2.28.1
requests-oauthlib 1.3.1
responses 0.18.0
rfc3339-validator 0.1.4
rfc3987 1.3.8
rsa 4.9
scanpy 1.9.1
scikit-allel 1.3.5
scikit-learn 1.1.2
scikit-plot 0.3.7
scipy 1.9.0
seaborn 0.11.2
Send2Trash 1.8.0
sentry-sdk 1.15.0
serializable 0.2.1
session-info 1.0.0
setproctitle 1.3.2
shap 0.41.0
simplejson 3.17.6
sklearn 0.0
slicer 0.0.7
smmap 5.0.0
sniffio 1.3.0
soupsieve 2.3.2.post1
stack-data 0.5.1
statsmodels 0.13.5
stdlib-list 0.8.0
swagger-spec-validator 2.7.4
tabulate 0.9.0
tensorboard 2.9.1
tensorboard-data-server 0.6.1
tensorboard-plugin-wit 1.8.1
tensorflow-addons 0.17.1
tensorflow-datasets 4.7.0
tensorflow-estimator 2.9.0
tensorflow-macos 2.9.2
tensorflow-metadata 1.10.0
tensorflow-metal 0.5.1
termcolor 1.1.0
terminado 0.16.0
textwrap3 0.9.2
threadpoolctl 3.1.0
tinycss2 1.2.1
tinytimer 0.0.0
toml 0.10.2
tomli 2.0.1
toolz 0.12.0
tornado 6.2
traitlets 5.5.0
twobitreader 3.1.7
typechecks 0.1.0
typeguard 2.13.3
typing_extensions 4.3.0
umap-learn 0.5.3
unicodedata2 14.0.0
uri-template 1.2.0
urllib3 1.26.11
venn 0.1.3
wandb 0.13.10
wcwidth 0.2.5
webcolors 1.12
webencodings 0.5.1
websocket-client 1.4.1
Werkzeug 2.2.2
widgetsnbextension 4.0.3
wrapt 1.14.1
xgboost 1.6.2
xxhash 3.2.0
yarl 1.8.2
I'm not sure what to tell you, the released version is not really relying on any non-standard packages other than numpy and matplotlib...
This behavior is caused by the following:
%matplotlib inline -> works well %matplotlib notebook-> broken
Unfortunately, in many cases I need the notebook backend for interactivity and I can't temporarily switch the backend, because it disables all the interactivity in my existing plots. It would be great if it could be made to work with the notebook backend.
I am assuming it works with the current version... Feel free to reopen or clarify in the PR mentioned above.