# Quick start 

## Set up environment
```
# clone the github repo and then type the following in the shell
conda env create -f environment.yml
# activate the enviornment 
conda activate pastaenv
```
## A quick example 
The example dataset can be downloaded from our github page under the folder `example_data`. 
The data can be extracted by
```
import pickle
file = open('test.pkl', 'rb')
sp_adata = pickle.load(file)
sc_adata = pickle.load(file)
cluster = pickle.load(file)
coords = pickle.load(file)
pthw_genes = pickle.load(file)
file.close()
```
The ST dataset (`sp_adata`) contains 15823 cells and 133 genes. 
The scRNA-seq dataset (`sc_adata`) contains 3000 cells and 712 genes. 
Both of them are in `h5ad` format. 
The cell type annotation and coordinates of the ST dataset can be found in `cluster` and `coords`. 
`pthw_genes` is a list of genes from a GOBP pathway. 

Then we can run the analysis using 
```
import os
sys.path.append('./pasta')
import __init__
import _version
import optimizer
import mapper
import utils

mapper.pp_adatas(sc_adata, sp_adata)
ad_map = mapper.mapping(sc_adata, sp_adata, genes, sp_coords=coords, ncell_thres=10,
    sp_celltypes=cluster["Cluster"], lambda_g2=2, num_epochs=500)
pthw_exp = utils.project_genes(adata_map=ad_map, adata_sc=sc_adata, pthw=genes)
```
If you would like to run the imputation for multiple pathways, you can use the `run_batch` function. 
```
# we still use the pickle file as an example
pathway = ["p1"] * (len(pthw) // 2) + ["p2"] * (len(pthw) - len(pthw) // 2)
pthw_d = pd.DataFrame({'gene': pthw, 'pathway': pathway}) # input to the run_batch function

# the pathway input to the run_batch function should be a dataframe contains two columns with name as "genes" (gene names) and "pathway" (pathway names)
result = utils.run_batch(sc_adata, sp_adata, pthw_d, sp_coords=coords, ncell_thres=10, lambda_1=1, lambda_2=1, lambda_3=1, lambda_4=1,
    sp_celltypes=cluster["Cluster"], num_epochs=500, folder="./test/")
# we ask users to provide a folder to write each pathway as a csv file
```