This code is prototype of a tool to allow users to represent a cell type taxonomy that as an interactive constellation plot. The code works by pre-computing the data necessary to render the interactive visualization, storing that data in an HDF5 file, and then using the cherrypy library to serve a small app on the user's local machine within which to visualize the constellation plot.
This tool is written purely in python. The installation instructions below, while minimal, assume you have a functioning python environment in which you want to install this tool and its dependencies.
To install this code, simply clone the repository and then, from the root directory of the repository run
pip install -e .
You will know you were successful if you can open a python shell and successfully run
import cell_type_constellations
import cell_type_mapper
The example script
examples/serialization_example.py
shows how to call a function that reads data from a single h5ad file and creates an HDF5 file that can be used to create an interactive constellation plot. The arguments of the function called in that script are defined in its docstring. See
src/cell_type_constellations/serialization/serialization.py
This tool comes with a simple web-like app that will allow you to
visualize and configure your constellation plots in any web browser.
The app works by scanning the app_data/ directory of this repository
and loading any .h5 files (created by the serialization example
above) for visualization. Just copy all of the constellation plot data
files you want to be able to visualize into that app_data/ directory and run
bash run_visualization.sh
you should see output like
(constellations) osxltFMD6W:cell_type_constellations scott.daniel$ bash run_visualization.sh
/Users/scott.daniel/miniconda3/envs/constellations/lib/python3.10/site-packages/cell_type_mapper/taxonomy/utils.py:245: UserWarning: This taxonomy has no mapping from leaf_node -> rows in the cell by gene matrix
warnings.warn("This taxonomy has no mapping from leaf_node -> rows "
[27/Nov/2024:15:42:24] ENGINE Listening for SIGTERM.
[27/Nov/2024:15:42:24] ENGINE Listening for SIGHUP.
[27/Nov/2024:15:42:24] ENGINE Listening for SIGUSR1.
[27/Nov/2024:15:42:24] ENGINE Bus STARTING
CherryPy Checker:
The Application mounted at '' has an empty config.
[27/Nov/2024:15:42:24] ENGINE Started monitor thread 'Autoreloader'.
[27/Nov/2024:15:42:24] ENGINE Serving on http://127.0.0.1:8080
[27/Nov/2024:15:42:24] ENGINE Bus STARTED
appear in your terminal window. The IP address in this line
[27/Nov/2024:15:42:24] ENGINE Serving on http://127.0.0.1:8080
is the IP address to point your browser towards. You should now be able to select one of your constellation plots to visualize.