aron0093 / cytopath Goto Github PK
View Code? Open in Web Editor NEWSimulation based inference of differentiation trajectories from RNA velocity fields.
License: BSD 3-Clause "New" or "Revised" License
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Multiple trajectories with the same start end clusters
Hello,
Thank you for building this tool. I just started using it and I am confused about the results I am getting. I am new to python and cytopath so will appreciate all your help!
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When I plot my trajectories I get 3 different trajectories with the same start and end clusters. Is there a way to resolve them to get just one trajectory?
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I am using my seurat clusters for sampling is that okay or should I use louvain clusters?
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Also, how can I project all my trajectories onto my umap as you did in the paper (Fig1. C.2)?
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Also my cell fate probability plot shows that all my cells along the trajectory have the same cell fate probability similar to cytopath_analysis_pancreatic_endocinogenesis.ipynb example when you have not set terminal clusters. What does this mean?
Thank you!
Data availability
Hello, I'm interested in using cytopath, and specifically your cd8 t cell dataset. Any chance the anndata file is available?
Thank you,
Adam
Running time for cytopath.trajectories
Hi there,
thanks for building this tool. I have been trying to reproduce the analysis of some of your examples (in particular the neonatal_mouse_inner_ear_burns.h5ad dataset) before running it on my data, all analysis steps are running well but I haven't managed to run the cytopath.trajectories function, as it have been running for an hour or more without further progress to what is shown on the attached screenshot.
I was wondering if this is expected behavior and if you have an estimated runtime.
For assistance, I am running this on an M1 MacBookPro with 8 cores and pasting below my environment details.
Thank you!
Anastasia
# Name Version Build Channel
alabaster 0.7.12 py_0 conda-forge
aniso8601 9.0.1 pypi_0 pypi
anndata 0.8.0 pyhd8ed1ab_1 conda-forge
anndata2ri 1.1 pypi_0 pypi
annoy 1.17.1 pypi_0 pypi
appnope 0.1.2 py38hecd8cb5_1001
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py38hca72f7f_0
arpack 3.7.0 hff0ca13_2 conda-forge
asttokens 2.0.5 pyhd3eb1b0_0
attrs 21.4.0 pyhd3eb1b0_0
babel 2.10.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyhd3eb1b0_0
backports-zoneinfo 0.2.1 pypi_0 pypi
beautifulsoup4 4.11.1 py38hecd8cb5_0
biomart 0.9.2 pypi_0 pypi
bleach 4.1.0 pyhd3eb1b0_0
brotli 1.0.9 h5eb16cf_7 conda-forge
brotli-bin 1.0.9 h5eb16cf_7 conda-forge
brotlipy 0.7.0 py38hed1de0f_1004 conda-forge
ca-certificates 2023.5.7 h8857fd0_0 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py38hc55c11b_0
chardet 4.0.0 pypi_0 pypi
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
click 8.1.3 pypi_0 pypi
cmake 3.24.1.1 pypi_0 pypi
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
cryptography 37.0.4 py38h0f8513e_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.32 pypi_0 pypi
cytopath 0.1.9 pypi_0 pypi
debugpy 1.5.1 py38he9d5cce_0
decorator 5.1.1 pyhd3eb1b0_0
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docutils 0.19 py38h50d1736_0 conda-forge
dunamai 1.13.0 pypi_0 pypi
entrypoints 0.4 py38hecd8cb5_0
et-xmlfile 1.1.0 pypi_0 pypi
executing 0.8.3 pyhd3eb1b0_0
fa2 0.3.5 pypi_0 pypi
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fbpca 1.0 pypi_0 pypi
fcsparser 0.2.4 pypi_0 pypi
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fonttools 4.37.1 py38hef030d1_0 conda-forge
freetype 2.10.4 h4cff582_1 conda-forge
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glpk 4.65 h0f52abe_1004 conda-forge
gmp 6.2.1 h2e338ed_0 conda-forge
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harmonypy 0.0.6 pypi_0 pypi
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hdf5 1.10.6 nompi_haae91d6_101 conda-forge
icu 58.2 h0a44026_1000 conda-forge
idna 2.10 pypi_0 pypi
igraph 0.9.10 hb215a4b_0 conda-forge
imageio 2.22.1 pypi_0 pypi
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importlib-metadata 4.11.4 py38h50d1736_0 conda-forge
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importlib_resources 5.2.0 pyhd3eb1b0_1
intervaltree 3.1.0 pypi_0 pypi
ipykernel 6.15.2 py38hecd8cb5_0
ipython 8.4.0 py38hecd8cb5_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 8.0.6 pypi_0 pypi
itsdangerous 2.1.2 pypi_0 pypi
jedi 0.18.1 py38hecd8cb5_1
jinja2 3.0.3 pyhd3eb1b0_0
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e hac89ed1_2 conda-forge
jsonschema 4.4.0 py38hecd8cb5_0
jupyter_client 7.3.5 py38hecd8cb5_0
jupyter_core 4.10.0 py38hecd8cb5_0
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libblas 3.9.0 8_openblas conda-forge
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libcblas 3.9.0 8_openblas conda-forge
libcxx 14.0.6 h9765a3e_0
libffi 3.3 hb1e8313_2
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libiconv 1.17 hac89ed1_0 conda-forge
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libllvm11 11.1.0 hd011deb_2 conda-forge
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libpng 1.6.37 h7cec526_2 conda-forge
libsodium 1.0.18 h1de35cc_0
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libxml2 2.9.14 hbf8cd5e_0
llvm-openmp 14.0.4 ha654fa7_0 conda-forge
llvmlite 0.38.0 py38h8346a28_0
loompy 3.0.7 pypi_0 pypi
louvain 0.7.1 py38h038c8f4_2 conda-forge
lz4-c 1.9.3 he49afe7_1 conda-forge
markupsafe 2.1.1 py38hca72f7f_0
matplotlib-base 3.5.3 py38h2894597_0 conda-forge
matplotlib-inline 0.1.6 py38hecd8cb5_0
metis 5.1.0 h2e338ed_1006 conda-forge
mistune 0.8.4 py38h1de35cc_1001
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nbstripout 0.6.1 pypi_0 pypi
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nest-asyncio 1.5.5 py38hecd8cb5_0
networkit 10.1 pypi_0 pypi
networkx 2.8.6 pyhd8ed1ab_0 conda-forge
notebook 6.4.12 py38hecd8cb5_0
numba 0.55.1 py38hae1ba45_0
numexpr 2.8.3 pypi_0 pypi
numpy 1.20.2 pypi_0 pypi
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olefile 0.46 pyh9f0ad1d_1 conda-forge
openjpeg 2.4.0 h6e7aa92_1 conda-forge
openpyxl 3.0.10 pypi_0 pypi
openssl 1.1.1u h8a1eda9_0 conda-forge
packaging 21.3 pyhd3eb1b0_0
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pandas 1.4.4 py38h5e0dbaf_0 conda-forge
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parso 0.8.3 pyhd3eb1b0_0
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pexpect 4.8.0 pyhd3eb1b0_3
phenograph 1.5.7 pypi_0 pypi
pickleshare 0.7.5 pyhd3eb1b0_1003
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pip 22.1.2 py38hecd8cb5_0
prometheus_client 0.14.1 py38hecd8cb5_0
prompt-toolkit 3.0.20 pyhd3eb1b0_0
psutil 5.9.0 py38hca72f7f_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
pyarrow 9.0.0 pypi_0 pypi
pycparser 2.21 pyhd3eb1b0_0
pygments 2.11.2 pyhd3eb1b0_0
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pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
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pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.8.13 hdfd78df_0
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.16.2 py38hecd8cb5_0
python-igraph 0.9.11 py38h1093a38_0 conda-forge
python-slugify 5.0.2 pypi_0 pypi
python_abi 3.8 2_cp38 conda-forge
pytz 2022.2.1 pyhd8ed1ab_0 conda-forge
pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi
pywavelets 1.3.0 pypi_0 pypi
pyzmq 23.2.0 py38he9d5cce_0
readline 8.1.2 hca72f7f_1
requests 2.25.1 pypi_0 pypi
rpy2 3.5.4 pypi_0 pypi
scanorama 1.7.2 pypi_0 pypi
scanpy 1.9.1 pyhd8ed1ab_0 conda-forge
scikit-image 0.19.3 pypi_0 pypi
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sklearn 0.0 pypi_0 pypi
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sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlite 3.39.2 h707629a_0
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tables 3.7.0 pypi_0 pypi
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tbb 2021.5.0 hb8565cd_2 conda-forge
terminado 0.13.1 py38hecd8cb5_0
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text-unidecode 1.3 pypi_0 pypi
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threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tifffile 2022.8.12 pypi_0 pypi
tk 8.6.12 h5d9f67b_0
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tqdm 4.64.1 pyhd8ed1ab_0 conda-forge
traitlets 5.1.1 pyhd3eb1b0_0
typing-extensions 4.3.0 py38hecd8cb5_0
typing_extensions 4.3.0 py38hecd8cb5_0
tzdata 2022.2 pypi_0 pypi
tzlocal 4.2 pypi_0 pypi
umap-learn 0.5.3 py38h50d1736_0 conda-forge
unicodedata2 14.0.0 py38hed1de0f_1 conda-forge
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
watermark 2.3.1 pypi_0 pypi
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xz 5.2.5 hca72f7f_1
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zipp 3.8.0 py38hecd8cb5_0
zlib 1.2.12 h4dc903c_3
zstd 1.4.9 h582d3a0_0 conda-forge
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