Planarian lineages: cell map from PAGA拟时序分析 monocle_paga拟时分析

https://nbviewer.org/github/rajewsky-lab/planarian_lineages/blob/master/paga/planaria.ipynb

https://github.com/rajewsky-lab/planarian_lineages/blob/master/run_monocle2.R

 https://github.com/rajewsky-lab/planarian_lineages/blob/master/paga/preprocessing.ipynb

This notebook reproduces the main cell map with its lineage relations. For this, it uses the Scanpy package.

All necessary files can be downloaded from the download section on https://shiny.mdc-berlin.de/psca/.

In [1]:

import numpy as np
import pandas as pd
import matplotlib.pyplot as pl
import scanpy.api as sc

sc.settings.verbosity = 2  # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.settings.set_figure_params(dpi=150)  # low dpi (dots per inch) yields small inline figures
sc.logging.print_versions()
results_file = './write/planaria.h5ad'

scanpy==1.0.3 anndata==0.5.8 numpy==1.13.1 scipy==1.0.0 pandas==0.22.0 scikit-learn==0.19.1 statsmodels==0.8.0 python-igraph==0.7.1 louvain==0.6.1 

Some plotting parameters.