zcang/commot

commot's Issues

Codes of simulation data generating

Hi Zixuan. Could you provide the codes for simulating the data? Or where should I find them?

Comparing cell-type-level communication scores across samples

Thank you for this wonderful tool!

I obtained cell-type-level CCC scores and their associated p-values for multiple samples through the following commands:

pathway = "ACTIVIN"
ct.tl.cluster_communication(adata, database_name = 'cellchat', pathway_name = pathway, clustering = 'cell_type', n_permutations = 100)
ccc_scores = adata.uns['commot_cluster-cell_type-cellchat-' + pathway]["communication_matrix"]
ccc_pvals = adata_disthr.uns['commot_cluster-cell_type-cellchat-' + pathway]["communication_pvalue"]

I found that even though prior data processing/normalization/analysis is uniform across samples, the CCC scores for the same (pathway, cell type 1, cell type 2) combo have quite distinct value distributions across different samples. CCC scores that are similarly significant (p-value = 0) can be very different in terms of magnitude across samples, making subsequent analysis and visualization difficult.

Therefore, I have the following questions:

Is it meaningful to compare the magnitude of CCC scores for the same cell type combination across samples?

• If not, what will be a good way to compare the COMMOT results across different samples?
• If so,
  • What is the possible range of communication_matrix?
  • Is communication_matrix normalized? Would you advise performing normalization/scaling to the scores before comparison? Should the scaling be on a sample level, on a (sample, pathway) level, or on a (sample, cell type 1, cell type 2) level?

Any advice will be much appreciated. Thanks again for your help!

Error installation rvlib

Hi,

I have a problem to install commot. It is a problem related to rvlib. I am using Windows 10. This is the error I got:

`Building wheels for collected packages: rvlib
Building wheel for rvlib (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [103 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-cpython-310
creating build\lib.win-amd64-cpython-310\rvlib
copying rvlib\specials.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib\univariate.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib\version.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib_init_.py -> build\lib.win-amd64-cpython-310\rvlib
running egg_info
writing rvlib.egg-info\PKG-INFO
writing dependency_links to rvlib.egg-info\dependency_links.txt
writing requirements to rvlib.egg-info\requires.txt
writing top-level names to rvlib.egg-info\top_level.txt
reading manifest file 'rvlib.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'rvlib.egg-info\SOURCES.txt'
copying rvlib\metadata.yaml -> build\lib.win-amd64-cpython-310\rvlib
running build_ext
generating cffi module 'build\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.c'
creating build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release
building 'rvlib._rmath_ffi' extension
creating build\temp.win-amd64-cpython-310\Release\build
creating build\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310\Release
creating build\temp.win-amd64-cpython-310\Release\src
"C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Isrc -Iinclude -IC:\Users\adjedi\Anaconda3\envs\commot-env\include -IC:\Users\adjedi\Anaconda3\envs\commot-env\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\cppwinrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" /Tcbuild\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.c /Fobuild\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.obj -DMATHLIB_STANDALONE -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
rvlib._rmath_ffi.c
include\Rconfig.h(16): warning C4005: 'HAVE_HYPOT': macro redefinition
C:\Users\adjedi\Anaconda3\envs\commot-env\include\pyconfig.h(61): note: see previous definition of 'HAVE_HYPOT'
"C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Isrc -Iinclude -IC:\Users\adjedi\Anaconda3\envs\commot-env\include -IC:\Users\adjedi\Anaconda3\envs\commot-env\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\cppwinrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" /Tcsrc\bd0.c /Fobuild\temp.win-amd64-cpython-310\Release\src\bd0.obj -DMATHLIB_STANDALONE -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
bd0.c
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(29): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(12): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(131): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(15): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1130): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1640): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1662): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1797): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1798): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1854): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2094): warning C4996: '_vsnwscanf_l': This function or variable may be unsafe. Consider using _vsnwscanf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2116): warning C4996: '_vsnwscanf_l': This function or variable may be unsafe. Consider using _vsnwscanf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2171): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(15): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1412): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1459): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1474): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1755): warning C4996: '_vsprintf_l': This function or variable may be unsafe. Consider using _vsprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1776): warning C4996: '_vsprintf_l': This function or variable may be unsafe. Consider using _vsprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1899): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2192): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2193): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2216): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2300): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2301): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2398): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2447): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(234): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(17): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(218): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(481): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(78): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(18): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(19): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(308): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(309): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(343): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1217): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1218): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1231): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1289): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1290): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1292): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1300): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1308): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1315): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1322): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1337): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1351): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1361): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): error C2124: divide or mod by zero
error: command 'C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe' failed with exit code 2
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for rvlib
Running setup.py clean for rvlib
Failed to build rvlib
Installing collected packages: rvlib, requests-futures, quantecon, python-Levenshtein, pygsp, pot, pandas, miniful, matplotlib, inequality, cligj, click-plugins, botocore, aws-requests-auth, statsmodels, seaborn, s3transfer, rasterio, pynndescent, mapclassify, libpysal, fst-pso, fiona, anndata, umap-learn, spreg, rasterstats, pyfume, pointpats, geopandas, esda, boto3, tobler, spvcm, spglm, spaghetti, scanpy, quilt3, momepy, giddy, FuzzyTM, access, spopt, splot, spint, segregation, mgwr, gensim, pysal, karateclub, commot
Running setup.py install for rvlib ... error
error: subprocess-exited-with-error

× Running setup.py install for rvlib did not run successfully.
│ exit code: 1
╰─> [105 lines of output]
running install
C:\Users\adjedi\Anaconda3\envs\commot-env\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build\lib.win-amd64-cpython-310
creating build\lib.win-amd64-cpython-310\rvlib
copying rvlib\specials.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib\univariate.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib\version.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib_init_.py -> build\lib.win-amd64-cpython-310\rvlib
running egg_info
writing rvlib.egg-info\PKG-INFO
writing dependency_links to rvlib.egg-info\dependency_links.txt
writing requirements to rvlib.egg-info\requires.txt
writing top-level names to rvlib.egg-info\top_level.txt
reading manifest file 'rvlib.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'rvlib.egg-info\SOURCES.txt'
copying rvlib\metadata.yaml -> build\lib.win-amd64-cpython-310\rvlib
running build_ext
generating cffi module 'build\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.c'
creating build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release
building 'rvlib._rmath_ffi' extension
creating build\temp.win-amd64-cpython-310\Release\build
creating build\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310\Release
creating build\temp.win-amd64-cpython-310\Release\src
"C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Isrc -Iinclude -IC:\Users\adjedi\Anaconda3\envs\commot-env\include -IC:\Users\adjedi\Anaconda3\envs\commot-env\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\cppwinrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" /Tcbuild\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.c /Fobuild\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.obj -DMATHLIB_STANDALONE -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
rvlib._rmath_ffi.c
include\Rconfig.h(16): warning C4005: 'HAVE_HYPOT': macro redefinition
C:\Users\adjedi\Anaconda3\envs\commot-env\include\pyconfig.h(61): note: see previous definition of 'HAVE_HYPOT'
"C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Isrc -Iinclude -IC:\Users\adjedi\Anaconda3\envs\commot-env\include -IC:\Users\adjedi\Anaconda3\envs\commot-env\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\cppwinrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" /Tcsrc\bd0.c /Fobuild\temp.win-amd64-cpython-310\Release\src\bd0.obj -DMATHLIB_STANDALONE -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
bd0.c
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(29): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(12): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(131): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(15): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1130): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1640): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1662): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1797): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1798): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1854): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2094): warning C4996: '_vsnwscanf_l': This function or variable may be unsafe. Consider using _vsnwscanf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2116): warning C4996: '_vsnwscanf_l': This function or variable may be unsafe. Consider using _vsnwscanf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2171): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(15): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1412): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1459): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1474): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1755): warning C4996: '_vsprintf_l': This function or variable may be unsafe. Consider using _vsprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1776): warning C4996: '_vsprintf_l': This function or variable may be unsafe. Consider using _vsprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1899): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2192): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2193): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2216): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2300): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2301): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2398): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2447): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(234): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(17): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(218): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(481): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(78): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(18): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(19): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(308): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(309): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(343): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1217): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1218): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1231): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1289): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1290): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1292): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1300): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1308): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1315): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1322): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1337): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1351): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1361): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): error C2124: divide or mod by zero
error: command 'C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe' failed with exit code 2
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> rvlib

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.`

Do you have any ideas to solve it ?

Thanks a lot,

Best

Question about understanding the output of cluster-cluster communication

Hi,

I just have one quick question about the output of tl.cluster_communication_spatial_permutation(). It provided both the communication score matrix and the communication p-value matrix. Since I found they were not symmetric matrices, I would like to check the meaning of the column name and row name: which one represents the sender clusters (of course, another should be the receiver)? I did not find the explanation in the tutorial, not sure if I missed something.

Thanks in advance!

Request for a parameter for a parallel task

Thank you for your outstanding contribution in the field of cell-cell communication for spatial transcriptome analysis.

As a Python novice, I have been attempting to apply ct.tl.spatial_communication to my own dataset, and have encountered two questions:

What is the recommended approach for running this function in parallel?
Could you explain the rationale behind restricting the distance threshold to 200μm?

I can't import commot

Hi developer:
I successful install commot in my new conda environment,but i can't import it.
Here is my code:

import commot as ct
Traceback (most recent call last):
File "", line 1, in
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/commot/init.py", line 5, in
from . import preprocessing as pp
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/commot/preprocessing/init.py", line 1, in
from ._infer_spatial import infer_spatial_information
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/commot/preprocessing/_infer_spatial.py", line 4, in
import scanpy as sc
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/scanpy/init.py", line 16, in
from . import plotting as pl
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/scanpy/plotting/init.py", line 1, in
from ._anndata import (
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/scanpy/plotting/_anndata.py", line 28, in
from . import _utils
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/scanpy/plotting/_utils.py", line 35, in
class _AxesSubplot(Axes, axes.SubplotBase, ABC):
TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases

Thanks for your attention!

IndexError: single positional indexer is out-of-bounds

Hi, Dr Cang,

COMMOT is an excellent tool for analyzing CCC in ST data.

I can run COMMOT on the sample data from your tutorial. However, I downloaded breast cancer visium data (i.e., filtered_feature_bc_matrix.h5) from
https://www.10xgenomics.com/resources/datasets/human-breast-cancer-block-a-section-1-1-standard-1-1-0, and analyzed it and got the following error.

adata = sc.read_visium("./test/",count_file='filtered_feature_bc_matrix.h5')
adata.var_names_make_unique()

sc.pp.normalize_total(adata, inplace=True)
sc.pp.log1p(adata)

LR=np.array([['Tgfb1', 'Tgfbr1_Tgfbr2', 'Tgfb_pathway'],
['Tgfb2', 'Tgfbr1_Tgfbr2', 'Tgfb_pathway'],
['Tgfb3', 'Tgfbr1_Tgfbr2', 'Tgfb_pathway'],
['Fgf1', 'Fgfr1', 'FGF_pathway'],
['Fgf1', 'Fgfr2', 'FGF_pathway']],dtype=str)
df_ligrec = pd.DataFrame(data=LR)

ct.tl.spatial_communication(adata, database_name='user_database', df_ligrec=df_ligrec, dis_thr=500, heteromeric=True, pathway_sum=True)

Traceback (most recent call last):
File "", line 1, in
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/commot/tools/_spatial_communication.py", line 418, in spatial_communication
model = CellCommunication(adata,
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/commot/tools/_spatial_communication.py", line 71, in init
tmp_recs = list(set(df_ligrec.iloc[:,1]))
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 925, in getitem
return self._getitem_tuple(key)
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 1506, in _getitem_tuple
self._has_valid_tuple(tup)
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 754, in _has_valid_tuple
self._validate_key(k, i)
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 1409, in _validate_key
self._validate_integer(key, axis)
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 1500, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds

Thanks.

Best,
Beibei

Please refer to 'igraph' instead of 'python-igraph'

Please refer to igraph instead of python-igraph in the following three locations:

https://github.com/search?q=repo%3Azcang%2FCOMMOT%20python-igraph&type=code

The reasoning is given in igraph/python-igraph#699

About 'ct.pl.plot_cell_communication'

Hi, zcang,

I have another question.

When I want to use 'ct.pl.plot_cell_communication' to plot 'sender' and 'receiver' on the same figure , I set 'ax' and got the following error:
__

I see that in function('plot_cell_signaling') , you use the fig, but after I set ax, fig cannot be input from('ct.pl.plot_cell_communication')

Or is there any other way that I can put these two pictures on the same picture？

Thank you very much!

ct.tl.communication_deg_detection error:Not all gene IDs are present in the models object.

hi, thanks for the tool! I have a question for you.
when I run 'ct.tl.communication_deg_detection' :
'df_deg, df_yhat = ct.tl.communication_deg_detection(adata,
database_name = 'cellchat', pathway_name='GRN', summary = 'receiver')'
some errors occurred: (i have no idea about this, looking forward to your reply!)
Traceback (most recent call last):
File "/dellfsqd2/ST_LBI/USER/zhaowandong/projects/wochong/05.test/ccc/A8_deg.py", line 18, in
df_deg, df_yhat = ct.tl.communication_deg_detection(adata,
File "/dellfsqd2/ST_LBI/USER/zhaowandong/Tools/anaconda3/envs/py3.8/lib/python3.8/site-packages/commot/tools/_downstream_analysis.py", line 168, in communication_deg_detection
ro.r(string_cluster)
File "/dellfsqd2/ST_LBI/USER/zhaowandong/Tools/anaconda3/envs/py3.8/lib/python3.8/site-packages/rpy2/robjects/init.py", line 501, in call
res, visible = rinterface.evalr_expr_with_visible( # type: ignore
File "/dellfsqd2/ST_LBI/USER/zhaowandong/Tools/anaconda3/envs/py3.8/lib/python3.8/site-packages/rpy2/rinterface.py", line 183, in evalr_expr_with_visible
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in .clusterExpressionPatterns(models = models, nPoints = nPoints, :
Not all gene IDs are present in the models object.

Error in communication_deg_detection

I have installed commot[tradeSeq], R3.6.3, and R package tradeSeq.
when running
ct.tl.communication_deg_detection(adata, database_name = 'testDB', pathway_name='true_pathway', summary = 'receiver')
the error comes out.

RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/opt/R/3.6.3/lib/R/library/methods/libs/methods.so':
libR.so: cannot open shared object file: No such file or directory

I've checked that '/opt/R/3.6.3/lib/R/library/methods/libs/methods.so' exists. I have tried to set directories of R library. And here is the output of%run -m rpy2.situation

rpy2 version:
3.4.2
Python version:
3.8.13 (default, Oct 21 2022, 23:50:54)
[GCC 11.2.0]
Looking for R's HOME:
Environment variable R_HOME: /opt/R/3.6.3/
Calling R RHOME: /opt/R/3.6.3/lib/R
Environment variable R_LIBS_USER: /opt/R/3.6.3/lib/R/library
Warning: The environment variable R_HOME differs from the default R in the PATH.
R's additions to LD_LIBRARY_PATH:
:/opt/R/3.6.3/lib/R/library/methods/libs:/opt/R/3.6.3/lib/R/library/
R version:
In the PATH: R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
include:
['/opt/R/3.6.3/lib/R/include']
libraries:
['R', 'pcre2-8', 'pcre', 'lzma', 'bz2', 'z', 'tirpc', 'rt', 'dl', 'm', 'icuuc', 'icui18n']
library_dirs:
['/usr/local/lib', '/opt/R/3.6.3/lib/R/lib']
extra_compile_args:
[]
extra_link_args:
['-Wl,--export-dynamic', '-fopenmp']

unable to install commot

Dear Developer,

I made several attempts to install commit using jupyter and spyder. However, it kept giving me an error message.

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for rvlib Running setup.py clean for rvlib Failed to build rvlib Installing collected packages: python-louvain, Levenshtein, rvlib, requests-futures, rasterio, quantecon, python-Levenshtein, python-igraph, pygsp, pot, pandas, leidenalg, inequality, fiona, deprecation, aws-requests-auth, rasterstats, pynndescent, mapclassify, libpysal, karateclub, geopandas, anndata, umap-learn, tobler, spreg, pointpats, momepy, esda, access, spvcm, spglm, spaghetti, scanpy, quilt3, giddy, spopt, splot, spint, segregation, mgwr, pysal, commot Running setup.py install for rvlib ... error error: subprocess-exited-with-error

× Running setup.py install for rvlib did not run successfully. │ exit code: 1 ╰─> [32 lines of output] running install /Users/ayuhutamisyarif/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.macosx-10.9-x86_64-cpython-39 creating build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/univariate.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/version.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/specials.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib running egg_info writing rvlib.egg-info/PKG-INFO writing dependency_links to rvlib.egg-info/dependency_links.txt writing requirements to rvlib.egg-info/requires.txt writing top-level names to rvlib.egg-info/top_level.txt reading manifest file 'rvlib.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'rvlib.egg-info/SOURCES.txt' copying rvlib/metadata.yaml -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib running build_ext generating cffi module 'build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.c' creating build/temp.macosx-10.9-x86_64-cpython-39 building 'rvlib._rmath_ffi' extension creating build/temp.macosx-10.9-x86_64-cpython-39/build creating build/temp.macosx-10.9-x86_64-cpython-39/build/temp.macosx-10.9-x86_64-cpython-39 creating build/temp.macosx-10.9-x86_64-cpython-39/src clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/ayuhutamisyarif/opt/anaconda3/include -arch x86_64 -I/Users/ayuhutamisyarif/opt/anaconda3/include -fPIC -O2 -isystem /Users/ayuhutamisyarif/opt/anaconda3/include -arch x86_64 -Isrc -Iinclude -I/Users/ayuhutamisyarif/opt/anaconda3/include/python3.9 -c build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.c -o build/temp.macosx-10.9-x86_64-cpython-39/build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.o -DMATHLIB_STANDALONE -std=c99 xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure

× Encountered error while trying to install package. ╰─> rvlib

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

I am very new to python and have no idea about this error. Any advice would be so much appreciated

Best,
Ayu

IndexError: list index out of range

Hi, when I want to use 'ct.pl.plot_cell_communication' to plot CCC, I got the following error:

Maybe you can help me solve it？

tradeseq is not working

Can you release a version without dependency on rpy2?
It seems rpy2 relies on a very specific combination of Python and R.
I have R 3.6 + Python 3.6, and R 4 + Python 3.10.
But I do not have the Python 3.7 + R 3.6 combination that is required of using tradeseq. I tried using conda, but ended up with a mess, because apparently pip tries to install the most up to date version of pre-requisite packages that either do not compile or are not supported in older Python 3.7.
All of these seem to be related to rpy2.

Can you put up a conda environment? Or release without rpy2?

Could you provide a full tutorial?

Hi zcang,

I am interested in this tool, it looks interesting. Could you provide a full tutorial? Thank you very much!

Questions about dis_thr

Hi COMMOT developers,
Thanks for providing such an awesome tool for us. I am now using COMMOT on my Visium data and having some questions about the distance threshold:

1. The default unit in adata.obsm['spatial'] is pixel but not μm, so the value you used in the tutorial is 200 pixel, but not 200μm, am I right?
2. I noted that you used 1000 μm for Visium data in the NM paper. How did you tranform the pixel to μm? What scale factor should be used?
3. Is there any general guidance on selecting this threshold? Or some recommended value?

Thanks in advance.

Yang

How to set 'dis_thr ' correctly?

Hi ,
When I use 'ct.tl.spatial_communication', I noticed that your description of ‘dis_thr’ in the tutorial is 'The threshold of spatial distance of signaling.', but I don't understand what the units of this number are, is it the number of cells? Or um?
And how do I set an appropriate distance for my organization? According to the max area?

Error when run "ct.tl.communication_deg_detection"

Hi, Thank you for such a great tool. I meet error when I run
df_deg, df_yhat = ct.tl.communication_deg_detection(adata_dis500, ... database_name = 'cellchat', pathway_name='SPP1', summary = 'receiver')

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/commot/tools/_downstream_analysis.py", line 154, in communication_deg_detection ro.r(string_fitGAM) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/__init__.py", line 438, in __call__ res = self.eval(p) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/functions.py", line 198, in __call__ return (super(SignatureTranslatedFunction, self) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/functions.py", line 126, in __call__ res = conversion.rpy2py(res) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/functools.py", line 874, in wrapper return dispatch(args[0].__class__)(*args, **kw) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 28, in rpy2py_s4 return rpy2py_single_cell_experiment(obj) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 95, in rpy2py_single_cell_experiment obs = rpy2py_data_frame(col_data) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 58, in rpy2py_data_frame columns = {k: rpy2py_vector(v) for k, v in slots["listData"].items()} File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 58, in <dictcomp> columns = {k: rpy2py_vector(v) for k, v in slots["listData"].items()} File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 49, in rpy2py_vector return pandas2ri.rpy2py(v) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/functools.py", line 874, in wrapper return dispatch(args[0].__class__)(*args, **kw) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/conversion.py", line 200, in _rpy2py raise NotImplementedError( NotImplementedError: Conversion 'rpy2py' not defined for objects of type '<class 'rpy2.robjects.methods.RS4'>'

Do you have any suggestions?