ELife publication: https://elifesciences.org/reviewed-preprints/87517
SPRAWL is a tool to identify subcellular RNA localization patterning from highly multiplexed spatial transcriptomics techniques such as MERFISH/Vizgen and SeqFish+
The SPRAWL methodology is introduced as a BioRXiv preprint
SPRAWL is available on PyPI as:
pip install subcellular-sprawl
The following can be used to test that sprawl has been installed correctly
from sprawl import vignette,plotting
import matplotlib.pyplot as plt
#load MERFISH sample data from included vignette
sample = vignette.m1s4_hdf5()
cells = sample.cells()
#plot the first cell with each gene in a different color
cell = cells[0]
fig,ax = plotting.plot_cell_3D(cell, rainbow=True)
ax.get_legend().remove() #legend is busy with 129 genes!
plt.show()
#plt.savefig('example_cell.png') #can save instead of show
plt.close()
There are more examples in the vignettes/ subdir
├── analysis
│ └── [jupyter notebooks for major analyses in paper]
├── Dockerfile
├── imgs
│ └── [images for README]
├── nf_pipeline
│ └── [nextflow singularity pipeline for running SPRAWL]
├── package
│ └── [SPRAWL python package with src/ and build/]
├── paper
│ └── [figures and text for sprawl paper]
├── preprocessing
│ └── [preprocessing nextflow scripts for spatial datasets]
├── README.md
│ └── [this file]
├── requirements_test.txt
│ └── [requirements for running pytest]
├── tests
│ └── [non-comprehensive unittests for sprawl]
└── vignettes
└── [jupyter notebooks showing how to use included package data]
The SPRAWL python package requires python version 3.6.1 or above and depends on the following packages which are automatically installed along with SPRAWL
- numpy >= 1.19
- pandas >= 1.1
- scipy >= 1.5
- statsmodels >= 0.12
- shapely >= 1.8
- matplotlib >= 3.3
- seaborn >= 0.11
- h5py >= 2.10
- importlib_resources >= 5.4
- click >= 8.0
- pysam >= 0.19