MIXSCAPE - ms.plot_barplot(mdata["rna"], guide_rna_column="NT") shows no graph output with papalexi_2021 provided data

VittoriaDBocchi commented 2 days ago

Report

when runnung ms.plot_barplot(mdata["rna"], guide_rna_column="NT") during the mixscape pipeline with the data provided by the authors (mdata = pt.dt.papalexi_2021()) I get no output: <Figure size 200x200 with 0 Axes> None

Version information

anndata 0.10.7 matplotlib 3.8.4 mudata 0.2.3 muon 0.1.6 numpy 1.26.4 pandas 2.2.2 pertpy 0.7.0 scanpy 1.10.1 scipy 1.13.0 seaborn 0.13.2 session_info 1.0.0

PIL 10.3.0 absl NA adjustText 1.1.1 arrow 1.3.0 arviz 0.18.0 asttokens NA attr 23.2.0 backcall 0.2.0 blitzgsea NA certifi 2024.02.02 chardet 5.2.0 charset_normalizer 3.3.2 chex 0.1.86 colorama 0.4.6 comm 0.1.2 contextlib2 NA custom_inherit 2.4.1 cycler 0.12.1 cython_runtime NA dateutil 2.8.2 debugpy 1.6.7 decorator 5.1.1 decoupler 1.6.0 docrep 0.3.2 etils 1.8.0 executing 0.8.3 flax 0.8.3 fsspec 2024.3.1 h5py 3.11.0 idna 3.7 igraph 0.11.5 importlib_resources NA ipykernel 6.25.0 jax 0.4.27 jaxlib 0.4.27 jaxopt NA jedi 0.18.1 joblib 1.4.2 kiwisolver 1.4.5 legacy_api_wrap NA leidenalg 0.10.2 lightning 2.1.4 lightning_fabric 2.2.4 lightning_utilities 0.11.2 llvmlite 0.42.0 matplotlib_inline 0.1.6 ml_collections NA ml_dtypes 0.4.0 mpl_toolkits NA mpmath 1.3.0 msgpack 1.0.8 multipledispatch 0.6.0 natsort 8.4.0 numba 0.59.1 numpyro 0.14.0 opt_einsum v3.3.0 optax 0.2.2 ott 0.4.6 packaging 23.1 parso 0.8.3 patsy 0.5.6 pexpect 4.8.0 pickleshare 0.7.5 pkg_resources NA platformdirs 3.10.0 ply 3.11 png 0.20220715.0 pretty_errors 1.2.25 prompt_toolkit 3.0.36 psutil 5.9.0 ptyprocess 0.7.0 pubchempy 1.0.4 pure_eval 0.2.2 pyarrow 16.0.0 pydev_ipython NA pydevconsole NA pydevd 2.9.5 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygments 2.15.1 pynndescent 0.5.12 pyomo 6.7.1 pyparsing 3.1.2 pyro 1.9.0 pytorch_lightning 2.2.4 pytz 2024.1 reportlab 4.2.0 requests 2.31.0 rich NA scvi 1.1.2 six 1.16.0 sklearn 1.4.2 skmisc 0.3.1 sparsecca 0.3.1 stack_data 0.2.0 statsmodels 0.14.2 texttable 1.7.0 threadpoolctl 3.5.0 toolz 0.12.1 torch 2.3.0+cu121 torchgen NA torchmetrics 1.4.0 tornado 6.3.3 toyplot 1.0.3 toytree 2.0.5 tqdm 4.66.4 traitlets 5.7.1 tree 0.1.8 typing_extensions NA umap 0.5.6 urllib3 2.2.1 wcwidth 0.2.5 xarray 2024.3.0 xarray_einstats 0.7.0 yaml 6.0.1 zmq 25.1.0

IPython 8.15.0 jupyter_client 8.6.0 jupyter_core 5.5.0

Python 3.11.5 (main, Sep 11 2023, 13:54:46) [GCC 11.2.0] Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-glibc2.17

Session information updated at 2024-09-19 15:21

Zethson commented 2 days ago

Thanks! We'll look into it

Zethson commented 2 days ago

Ohh, I see that you're running version 0.7.0. Could you please upgrade to the latest version with pip install -U pertpy to see whether the issue persists?

VittoriaDBocchi commented 2 days ago

Thank you for the prompt response. It does persist even with pertpy version 0.9.4. I notice that in the previous step (ms.mixscape(adata=mdata["rna"], control="sg_non_targeting", labels="GuidesGene", layer="X_pert") ) I get this warning: RuntimeWarning: invalid value encountered in log2 self.stats[group_name, "logfoldchanges"] = np.log2( ...envs/pertpy/lib/python3.11/site-packages/scanpy/tools/_rank_genes_groups.py:455: PerformanceWarning: DataFrame is highly fragmented. This is usually the result of calling frame.insert many times, which has poor performance. Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use newframe = frame.copy() self.stats[group_name, "logfoldchanges"] = np.log2( finished: added to .uns['rank_genes_groups'] 'names', sorted np.recarray to be indexed by group ids 'scores', sorted np.recarray to be indexed by group ids 'logfoldchanges', sorted np.recarray to be indexed by group ids 'pvals', sorted np.recarray to be indexed by group ids 'pvals_adj', sorted np.recarray to be indexed by group ids (0:00:19) ...envs/pertpy/lib/python3.11/site-packages/pertpy/tools/_mixscape.py:318: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '[0.74430524 0.92261884 0.78700851 0.8451406 0.24272429 0.17320238... could this have anything to do with it? Thanks again!

Lilly-May commented 2 days ago

Hi @VittoriaDBocchi! Thanks for testing with the updated pertpy version. I've just tested it myself but everything works fine on my end. When I run the example below, the plot is properly displayed:

mdata = pt.dt.papalexi_2021()
ms_pt = pt.tl.Mixscape()
ms_pt.perturbation_signature(mdata["rna"], "perturbation", "NT", "replicate")
ms_pt.mixscape(adata=mdata["rna"], control="NT", labels="gene_target", layer="X_pert")
ms_pt.plot_barplot(mdata["rna"], guide_rna_column="NT")

Did you run the exact same code? One possible issue I can think of is that the generated plot is quite large. How are you running the code— in a Jupyter notebook? Have large plots caused any issues for you before?

scverse / pertpy