fix errors

Author: WPZgithub

README.md

@@ -40,10 +40,20 @@ The following packages are required to be able to run this code:
   - PRROC (R package)
   - slingshot (R package)
   - MAST (R package)
+### Setup an environment
+```
+conda create -y --name CEFCON python=3.10
+conda activate CEFCON
+```
 ### Install using pip
 ```
 pip install git+https://github.com/WPZgithub/CEFCON.git
 ```
+### Install R and the required packages
+```
+conda install -y -c conda-forge r
+R --no-save -q < r_env.R
+```
 
 ### Using GUROBI
 
@@ -94,6 +104,11 @@ All the input data in the paper can be downloaded from [here](https://zenodo.org
 ```python
 import cefcon as cf
 
+# We assume you have an Anndata object containing scRNA-seq data, cell lineages information,
+# and gene differential expression levels (optional).
+# We also assume you have a pandas dataframe containing the prior gene interaction network
+# in edgelist format.
+
 # Data preparation
 data = cf.data_preparation(adata, prior_network)
 

r_env.R

@@ -0,0 +1,6 @@
+install.packages('PRROC', repos="https://cran.r-project.org/")
+install.packages('data.table', repos="https://cran.r-project.org/")
+
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager", repos="https://cran.r-project.org/")
+BiocManager::install(c("slingshot", "MAST"))

setup.py

@@ -38,7 +38,7 @@ def readme():
         'matplotlib-venn',
         'seaborn',
         'biomart',
-        'r',
+        #'r',
         'rpy2',
     ],
     # package_dir={'cefcon':'cefcon'},