Created
October 12, 2018 08:10
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Scanpy scatter plotting circles
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| name: scanpy_scatter_ring | |
| channels: | |
| - defaults | |
| - r | |
| - bioconda | |
| - conda-forge | |
| dependencies: | |
| - anndata=0.6.10=py_0 | |
| - igraph=0.7.1=hcc8e21d_5 | |
| - louvain=0.6.1=py36hfc679d8_1 | |
| - python-igraph=0.7.1.post6=py36h470a237_5 | |
| - backcall=0.1.0=py36_0 | |
| - blas=1.0=mkl | |
| - blosc=1.14.4=hdbcaa40_0 | |
| - bzip2=1.0.6=h14c3975_5 | |
| - ca-certificates=2018.03.07=0 | |
| - cairo=1.14.12=h8948797_3 | |
| - certifi=2018.8.24=py36_1 | |
| - cycler=0.10.0=py36_0 | |
| - dbus=1.13.2=h714fa37_1 | |
| - decorator=4.3.0=py36_0 | |
| - expat=2.2.6=he6710b0_0 | |
| - fontconfig=2.13.0=h9420a91_0 | |
| - freetype=2.9.1=h8a8886c_1 | |
| - glib=2.56.2=hd408876_0 | |
| - gmp=6.1.2=h6c8ec71_1 | |
| - gst-plugins-base=1.14.0=hbbd80ab_1 | |
| - gstreamer=1.14.0=hb453b48_1 | |
| - h5py=2.8.0=py36h989c5e5_3 | |
| - hdf5=1.10.2=hba1933b_1 | |
| - icu=58.2=h9c2bf20_1 | |
| - intel-openmp=2019.0=118 | |
| - ipython=7.0.1=py36h39e3cac_0 | |
| - ipython_genutils=0.2.0=py36_0 | |
| - jedi=0.13.1=py36_0 | |
| - jpeg=9b=h024ee3a_2 | |
| - kiwisolver=1.0.1=py36hf484d3e_0 | |
| - libedit=3.1.20170329=h6b74fdf_2 | |
| - libffi=3.2.1=hd88cf55_4 | |
| - libgcc-ng=8.2.0=hdf63c60_1 | |
| - libgfortran-ng=7.3.0=hdf63c60_0 | |
| - libiconv=1.15=h63c8f33_5 | |
| - libpng=1.6.34=hb9fc6fc_0 | |
| - libstdcxx-ng=8.2.0=hdf63c60_1 | |
| - libuuid=1.0.3=h1bed415_2 | |
| - libxcb=1.13=h1bed415_1 | |
| - libxml2=2.9.8=h26e45fe_1 | |
| - llvmlite=0.25.0=py36hd408876_0 | |
| - lzo=2.10=h49e0be7_2 | |
| - matplotlib=3.0.0=py36h5429711_0 | |
| - mkl=2019.0=118 | |
| - mkl_fft=1.0.6=py36h7dd41cf_0 | |
| - mkl_random=1.0.1=py36h4414c95_1 | |
| - natsort=5.4.0=py36_0 | |
| - ncurses=6.1=hf484d3e_0 | |
| - networkx=2.2=py36_1 | |
| - numba=0.40.0=py36h962f231_0 | |
| - numexpr=2.6.8=py36hd89afb7_0 | |
| - numpy=1.15.2=py36h1d66e8a_1 | |
| - numpy-base=1.15.2=py36h81de0dd_1 | |
| - openssl=1.0.2p=h14c3975_0 | |
| - pandas=0.23.4=py36h04863e7_0 | |
| - parso=0.3.1=py36_0 | |
| - patsy=0.5.0=py36_0 | |
| - pcre=8.42=h439df22_0 | |
| - pexpect=4.6.0=py36_0 | |
| - pickleshare=0.7.5=py36_0 | |
| - pip=10.0.1=py36_0 | |
| - pixman=0.34.0=hceecf20_3 | |
| - prompt_toolkit=2.0.5=py36_0 | |
| - ptyprocess=0.6.0=py36_0 | |
| - pycairo=1.17.1=py36h2a1e443_0 | |
| - pygments=2.2.0=py36_0 | |
| - pyparsing=2.2.2=py36_0 | |
| - pyqt=5.9.2=py36h05f1152_2 | |
| - pytables=3.4.4=py36ha205bf6_0 | |
| - python=3.6.6=h6e4f718_2 | |
| - python-dateutil=2.7.3=py36_0 | |
| - pytz=2018.5=py36_0 | |
| - qt=5.9.6=h8703b6f_2 | |
| - readline=7.0=h7b6447c_5 | |
| - scikit-learn=0.20.0=py36h4989274_1 | |
| - scipy=1.1.0=py36hfa4b5c9_1 | |
| - seaborn=0.9.0=py36_0 | |
| - setuptools=40.4.3=py36_0 | |
| - simplegeneric=0.8.1=py36_2 | |
| - sip=4.19.8=py36hf484d3e_0 | |
| - six=1.11.0=py36_1 | |
| - snappy=1.1.7=hbae5bb6_3 | |
| - sqlite=3.25.2=h7b6447c_0 | |
| - statsmodels=0.9.0=py36h035aef0_0 | |
| - tk=8.6.8=hbc83047_0 | |
| - tornado=5.1.1=py36h7b6447c_0 | |
| - traitlets=4.3.2=py36_0 | |
| - wcwidth=0.1.7=py36_0 | |
| - wheel=0.32.1=py36_0 | |
| - xz=5.2.4=h14c3975_4 | |
| - zlib=1.2.11=ha838bed_2 | |
| - pip: | |
| - joblib==0.12.5 | |
| - scanpy==1.3.2 | |
| - tables==3.4.4 | |
| prefix: /scratch-new/isaacv/miniconda3/envs/scanpy_scatter_ring | |
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| import scanpy.api as sc | |
| import numpy as np | |
| import pandas as pd | |
| sc.set_figure_params(dpi=300, dpi_save=300) # Makes it more visible | |
| N = 1000 | |
| M = 2000 | |
| adata = sc.AnnData( | |
| X=np.random.random_sample((N, M)), | |
| obs=pd.DataFrame({"a": np.random.randint(0, 2, N)}) | |
| ) | |
| adata.obs["a"] = adata.obs["a"].astype(str) | |
| sc.pp.pca(adata) | |
| sc.pl.pca(adata, color="a", size=0.1, save="test.pdf") |
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| name: scanpy_scatter_ring | |
| channels: | |
| - bioconda | |
| - defaults | |
| - conda-forge | |
| - r | |
| dependencies: | |
| - anndata=0.6.10=py_0 | |
| - libffi=3.2.1=1 | |
| - igraph=0.7.1=hcc8e21d_5 | |
| - louvain=0.6.1=py36hfc679d8_1 | |
| - python-igraph=0.7.1.post6=py36_4 | |
| - appnope=0.1.0=py36hf537a9a_0 | |
| - backcall=0.1.0=py36_0 | |
| - blas=1.0=mkl | |
| - blosc=1.14.4=hd9629dc_0 | |
| - bzip2=1.0.6=h1de35cc_5 | |
| - ca-certificates=2018.03.07=0 | |
| - cairo=1.14.12=hc4e6be7_4 | |
| - certifi=2018.8.24=py36_1 | |
| - cycler=0.10.0=py36hfc81398_0 | |
| - decorator=4.3.0=py36_0 | |
| - fontconfig=2.13.0=h5d5b041_1 | |
| - freetype=2.9.1=hb4e5f40_0 | |
| - gettext=0.19.8.1=h15daf44_3 | |
| - glib=2.56.2=hd9629dc_0 | |
| - gmp=6.1.2=hb37e062_1 | |
| - h5py=2.8.0=py36h878fce3_3 | |
| - hdf5=1.10.2=hfa1e0ec_1 | |
| - icu=58.2=h4b95b61_1 | |
| - intel-openmp=2019.0=118 | |
| - ipython=7.0.1=py36h39e3cac_0 | |
| - ipython_genutils=0.2.0=py36h241746c_0 | |
| - jedi=0.13.1=py36_0 | |
| - kiwisolver=1.0.1=py36h0a44026_0 | |
| - libcxx=4.0.1=h579ed51_0 | |
| - libcxxabi=4.0.1=hebd6815_0 | |
| - libedit=3.1.20170329=hb402a30_2 | |
| - libgfortran=3.0.1=h93005f0_2 | |
| - libgfortran-ng=3.0.1=h93005f0_2 | |
| - libiconv=1.15=hdd342a3_7 | |
| - libpng=1.6.34=he12f830_0 | |
| - libxml2=2.9.8=hab757c2_1 | |
| - llvmlite=0.25.0=py36h8c7ce04_0 | |
| - lzo=2.10=h362108e_2 | |
| - matplotlib=3.0.0=py36h54f8f79_0 | |
| - mkl=2019.0=118 | |
| - mkl_fft=1.0.6=py36hb8a8100_0 | |
| - mkl_random=1.0.1=py36h5d10147_1 | |
| - natsort=5.4.0=py36_0 | |
| - ncurses=6.1=h0a44026_0 | |
| - networkx=2.2=py36_1 | |
| - numba=0.40.0=py36h6440ff4_0 | |
| - numexpr=2.6.8=py36h1dc9127_0 | |
| - numpy=1.15.2=py36h6a91979_1 | |
| - numpy-base=1.15.2=py36h8a80b8c_1 | |
| - openssl=1.0.2p=h1de35cc_0 | |
| - pandas=0.23.4=py36h6440ff4_0 | |
| - parso=0.3.1=py36_0 | |
| - patsy=0.5.0=py36_0 | |
| - pcre=8.42=h378b8a2_0 | |
| - pexpect=4.6.0=py36_0 | |
| - pickleshare=0.7.5=py36_0 | |
| - pip=10.0.1=py36_0 | |
| - pixman=0.34.0=hca0a616_3 | |
| - prompt_toolkit=2.0.5=py36_0 | |
| - ptyprocess=0.6.0=py36_0 | |
| - pycairo=1.17.1=py36ha54c0a8_0 | |
| - pygments=2.2.0=py36h240cd3f_0 | |
| - pyparsing=2.2.2=py36_0 | |
| - pytables=3.4.4=py36h13cba08_0 | |
| - python=3.6.6=hc167b69_0 | |
| - python-dateutil=2.7.3=py36_0 | |
| - pytz=2018.5=py36_0 | |
| - readline=7.0=h1de35cc_5 | |
| - scikit-learn=0.20.0=py36h4f467ca_1 | |
| - scipy=1.1.0=py36h28f7352_1 | |
| - seaborn=0.9.0=py36_0 | |
| - setuptools=40.4.3=py36_0 | |
| - simplegeneric=0.8.1=py36_2 | |
| - six=1.11.0=py36_1 | |
| - snappy=1.1.7=he62c110_3 | |
| - sqlite=3.25.2=ha441bb4_0 | |
| - statsmodels=0.9.0=py36h1d22016_0 | |
| - tk=8.6.8=ha441bb4_0 | |
| - tornado=5.1.1=py36h1de35cc_0 | |
| - traitlets=4.3.2=py36h65bd3ce_0 | |
| - wcwidth=0.1.7=py36h8c6ec74_0 | |
| - wheel=0.32.1=py36_0 | |
| - xz=5.2.4=h1de35cc_4 | |
| - zlib=1.2.11=hf3cbc9b_2 | |
| - pip: | |
| - joblib==0.12.5 | |
| - scanpy==1.3.2 | |
| - tables==3.4.4 | |
| prefix: /Users/isaac/miniconda3/envs/scanpy_scatter_ring | |
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