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Teichlab / cellphonedb

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Question about plotting #198

Closed evenDDDDD closed 3 years ago

evenDDDDD commented 4 years ago

Hello, CellPhoneDB is a great software. I have a small problem when I use mean.txt and pvalue.txt to draw pictures. This is my code and error:

cellphonedb plot dot_plot --means-path ./out/means.txt --pvalues-path ./out/pvalues.txt --output-path ./out_plot

./lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.cluster.k_means_ module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API. warnings.warn(message, FutureWarning) [ ][APP][09/08/20-15:02:43][ERROR] Unexpected error Traceback (most recent call last): File "./lib/python3.6/site-packages/cellphonedb/src/api_endpoints/terminal_api/plot_terminal_api_endpoints/plot_terminal_commands.py", line 38, in dot_plot columns=columns) File "./lib/python3.6/site-packages/cellphonedb/src/plotters/r_plotter.py", line 35, in wrapper from rpy2.rinterface_lib.embedded import RRuntimeError File "./lib/python3.6/site-packages/rpy2/rinterface_lib/embedded.py", line 7, in <module> from . import openrlib File "./lib/python3.6/site-packages/rpy2/rinterface_lib/openrlib.py", line 21, in <module> rlib = _dlopen_rlib(R_HOME) File "./lib/python3.6/site-packages/rpy2/rinterface_lib/openrlib.py", line 17, in _dlopen_rlib rlib = ffi.dlopen(lib_path) OSError: cannot load library '/opt/R-3.6.1/lib/libR.so': /opt/R-3.6.1/lib/libR.so: cannot open shared object file: No such file or directory I don’t know why this problem occurred, I installed the latest version of cellphonedb and R v3.6.3. Expect a reply! Thank you!

YZYwoazzzzz commented 3 years ago

Hi, Do you solve this problem, any ideas? I also meet this problem. thx

YZYwoazzzzz commented 3 years ago

please check your count matirx发自我的华为手机-------- 原始邮件 --------发件人： beemilmlo notifications@github.com日期： 2020年10月6日周二 晚上9:34收件人： Teichlab/cellphonedb cellphonedb@noreply.github.com抄送： YZYwoazzzzz 424463870@qq.com, Comment comment@noreply.github.com主 题： Re: [Teichlab/cellphonedb] Question about plotting (#198) Hello, I am also wondering how to fix this. Have you made any progress? Thanks, RL

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arielyh commented 3 years ago

Hi CellphoneDB team,

We all have the same issue and we would like to follow up about the progress. Do you know how to fix the following Error? Thank you very much. OSError: cannot load library '/opt/R-3.6.1/lib/libR.so': /opt/R-3.6.1/lib/libR.so: cannot open shared object file: No such file or directory

prete commented 3 years ago

Hi @evenDDDDD @YZYwoazzzzz @arielyh this most likely caused by rpy2 looking for the shared object in the wrong place or your LD_LIBRARY_PATH not being set correctly. See https://github.com/rpy2/rpy2/issues/675

You can create a conda environment instead of using virtualenv and that will include R and all it dependencis. Follow the instructions on how to create a conda environment from this comment.

Alternatively, if you can't create a new conda env you can try running the plotting scripts manually as described here.