search

aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
447 stars 183 forks source link

Binary heatmap #250

Open wangjiawen2013 opened 3 years ago

wangjiawen2013 commented 3 years ago

Hi, How to generate binary heatmap used in your nature protocol paper (A scalable SCENIC workflow for single-cell gene regulatory network analysis, Fig.13)? It seems that it cannot be generated with pyscenic itself. image

jpcartailler commented 3 years ago

Hi - not the author, but you should look at the Jupyter notebook below, which has that exact plot and the context/code with which to generate it: https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/SCENIC%20Protocol%20-%20Case%20study%20-%20Cancer%20data%20sets.ipynb

Note - pySCENIC is used to generate the input data to plot this with, but will not plot if for you