Create node embedding

The aim of this section is to create the node embedding of SRT of spage2vec

Work Flow

Requirements

This script is a python script,and following package are required: see yml

Use the script

This script can create node embedding of spatial transcriptome.What is node embedding ,see work Flow or see spage2vec. If you want to generate the node of embedding of your own spatoal transcriptome data,you can use this script.

If you want tu use this script,you should provide two txt of your own spatial transcriptome data.

1. The spatial transcriptome of genelist. see genelist.The Q value is the probability of the gene belong to this cell.The parentCell is the cell.
2. The spatial transcriptome of taglist. see taglist

If you prepare the tow matrix,you can compute the SVG list by follow command

$ python creat_node_embedding.py --barcodes_df=genelist.csv --taglist_df=taglist.csv

The result of comand is node_embedding.npy.The resule can be used to downstream analysis.

Downstream

The aim of this section is to analysis the node embedding.

Work Flow

Requirement

This script is a python script,and following package are required: see yml

Use the script

This script can analysis the node embedding.

If you want to use this script,you should provide three files of your own spatial transcriptome data.

1. The spatial transcriptome of genelist. see genelist.The Q value is the probability of the gene belong to this cell.The parentCell is the cell.
2. The spatial transcriptome of taglist. see taglist
3. The node embedding.see node_embedding.npy

If you prepare the three file,you can analysis by follow command

$ python plot.py --barcodes_df=genelist.csv --taglist_df=taglist.csv --node_embedding=node_embedding.npy

This script will generate four png.

gene.png

embebding_spot.png

jubu.png

fangda.png