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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
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ValueError: 'vertices' must be a 2D list or array with shape Nx2 #195

Closed tang191024 closed 3 years ago

tang191024 commented 4 years ago

Hi! First of all thanks for developing this tools. Unfortunately I'm failing to run it and I am getting the following error dump:

Traceback (most recent call last): File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/bin/NanoPlot", line 6, in from nanoplot.NanoPlot import main File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 20, in import nanoplot.utils as utils File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/nanoplot/utils.py", line 9, in import pandas as pd File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/init.py", line 55, in from pandas.core.api import ( File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/core/api.py", line 24, in from pandas.core.groupby import Grouper, NamedAgg File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/core/groupby/init.py", line 1, in from pandas.core.groupby.generic import ( # noqa: F401 File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/core/groupby/generic.py", line 44, in from pandas.core.frame import DataFrame File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/core/frame.py", line 115, in from pandas.core.series import Series File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/core/series.py", line 84, in import pandas.plotting File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/plotting/init.py", line 59, in from pandas.plotting._core import ( File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/plotting/_core.py", line 17, in import pandas.plotting._matplotlib # noqa File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/plotting/_matplotlib/init.py", line 3, in from pandas.plotting._matplotlib.boxplot import ( File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/plotting/_matplotlib/boxplot.py", line 14, in from pandas.plotting._matplotlib.core import LinePlot, MPLPlot File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/plotting/_matplotlib/core.py", line 34, in from pandas.plotting._matplotlib.tools import ( File "/home/dq-lab/miniconda3/envs/ont_tutorial_sv/lib/python3.6/site-packages/pandas/plotting/_matplotlib/tools.py", line 5, in import matplotlib.table File "/home/dq-lab/.local/lib/python3.6/site-packages/matplotlib/table.py", line 24, in from .patches import Rectangle File "/home/dq-lab/.local/lib/python3.6/site-packages/matplotlib/patches.py", line 11, in from . import artist, cbook, colors, docstring, lines as mlines, transforms File "/home/dq-lab/.local/lib/python3.6/site-packages/matplotlib/lines.py", line 16, in from .markers import MarkerStyle File "/home/dq-lab/.local/lib/python3.6/site-packages/matplotlib/markers.py", line 162, in _empty_path = Path(np.empty((0, 2))) File "/home/dq-lab/.local/lib/python3.6/site-packages/matplotlib/path.py", line 130, in init "'vertices' must be a 2D list or array with shape Nx2") ValueError: 'vertices' must be a 2D list or array with shape Nx2

Any help would be appreciated.

Thanks!

wdecoster commented 4 years ago

This error seems to arise already before executing any code from NanoPlot itself, but when importing pandas, and derives all the way down to matplotlib. Odd.

Could you tell me how you installed NanoPlot? What do you get if you do the following:


python -c "import pandas ; print(pandas.__version__)"
python -c "import matplotlib ; print(matplotlib.__version__)"
tang191024 commented 4 years ago

Thanks for reply！ I install Nanoplot by "conda install nanoplot==1.28.2". But i have upgrade it to 1.31.0 by "pip install nanoplot -U" Now,when i run command:python -c "import pandas ; print(pandas.version)" i get "1.1.0" and "3.3.0" when Executing python -c "import matplotlib ; print(matplotlib.version)".

wdecoster commented 4 years ago

It's generally not recommended to install with conda and upgrade with pip, or vice versa. If you use conda to install then you probably should use conda to upgrade as well. I'm not sure if that is the cause, but to exclude that could you uninstall with pip, check the version of NanoPlot again and see if it works? After that you can upgrade with conda...