Pristina atlas analysis 0 Solo.ipynb

{"cells":[{"cell_type":"markdown","id":"432a007c","metadata":{"id":"432a007c"},"source":["# Installing scvi-tools"]},{"cell_type":"code","execution_count":null,"id":"64c064e5","metadata":{"id":"64c064e5"},"outputs":[],"source":["!pip install scvi-tools"]},{"cell_type":"markdown","id":"b7f1e9f5","metadata":{"id":"b7f1e9f5"},"source":["# Import all the necesary packages"]},{"cell_type":"code","execution_count":null,"id":"9acf76a4","metadata":{"id":"9acf76a4"},"outputs":[],"source":["import scvi\n","import numpy as np\n","import pandas as pd\n","import scanpy as sc\n","import os\n","import json\n","import loompy\n","import anndata\n","import leidenalg\n","import igraph as ig"]},{"cell_type":"code","execution_count":null,"id":"8ba9457d","metadata":{"id":"8ba9457d"},"outputs":[],"source":["from scvi.data import read_h5ad, read_loom\n","from scvi.model import SCVI\n","from scvi.external import SOLO"]},{"cell_type":"code","execution_count":null,"id":"cffd34c4","metadata":{"id":"cffd34c4"},"outputs":[],"source":["import session_info"]},{"cell_type":"code","execution_count":null,"id":"c4db6188","metadata":{"id":"c4db6188"},"outputs":[],"source":["session_info.show()"]},{"cell_type":"code","execution_count":null,"id":"199bce5d","metadata":{"id":"199bce5d"},"outputs":[],"source":["from scipy.sparse import csr_matrix"]},{"cell_type":"code","execution_count":null,"id":"e445f5ca","metadata":{"id":"e445f5ca"},"outputs":[],"source":["from matplotlib.pyplot import rc_context"]},{"cell_type":"code","execution_count":null,"id":"9350c7db","metadata":{"id":"9350c7db"},"outputs":[],"source":["sc.settings.verbosity = 4 \n","sc.logging.print_header()\n","sc.settings.set_figure_params(dpi=80, facecolor='white')"]},{"cell_type":"markdown","id":"760b8fe3","metadata":{"id":"760b8fe3"},"source":["# Load data and train the model"]},{"cell_type":"code","execution_count":null,"id":"b8e8e594","metadata":{"id":"b8e8e594"},"outputs":[],"source":["adata = sc.read_10x_mtx(\n","    \"./pristina/\",\n","    var_names='gene_symbols',\n","    cache=True)"]},{"cell_type":"code","execution_count":null,"id":"4e4dcdc0","metadata":{"id":"4e4dcdc0"},"outputs":[],"source":["adata.obs"]},{"cell_type":"code","execution_count":null,"id":"8c6e4f2d","metadata":{"id":"8c6e4f2d"},"outputs":[],"source":["adata = adata.copy()\n","scvi.model.SCVI.setup_anndata(adata)"]},{"cell_type":"code","execution_count":null,"id":"a5879107","metadata":{"scrolled":true,"id":"a5879107"},"outputs":[],"source":["vae = scvi.model.SCVI(adata)\n","vae.train()"]},{"cell_type":"code","execution_count":null,"id":"bf17ad5f","metadata":{"id":"bf17ad5f"},"outputs":[],"source":["solo = scvi.external.SOLO.from_scvi_model(vae)"]},{"cell_type":"code","execution_count":null,"id":"442788da","metadata":{"scrolled":false,"id":"442788da"},"outputs":[],"source":["solo.train(max_epochs=400, early_stopping=False)"]},{"cell_type":"code","execution_count":null,"id":"92e52966","metadata":{"id":"92e52966"},"outputs":[],"source":["solo_list= pd.DataFrame(solo.predict(include_simulated_doublets=False))"]},{"cell_type":"code","execution_count":null,"id":"ac7401af","metadata":{"id":"ac7401af"},"outputs":[],"source":["solo_list.to_excel(\"solo_ratio_multimappers 10.xlsx\")"]},{"cell_type":"code","execution_count":null,"id":"850885f8","metadata":{"id":"850885f8"},"outputs":[],"source":["vae"]},{"cell_type":"markdown","id":"62f4f99a","metadata":{"id":"62f4f99a"},"source":["## Uploading the data with cluster layers already calculated and check the location of the putative doublets"]},{"cell_type":"code","execution_count":null,"id":"7c89c66e","metadata":{"scrolled":true,"id":"7c89c66e"},"outputs":[],"source":["adata = anndata.read_h5ad('./pristina_atlas.h5ad')"]},{"cell_type":"code","execution_count":null,"id":"0b2bbaba","metadata":{"id":"0b2bbaba"},"outputs":[],"source":["with rc_context({'figure.figsize': (12, 12)}):\n","    sc.pl.umap(adata, color='solo_doublet', size = 30)"]},{"cell_type":"code","execution_count":null,"id":"f1eb7703","metadata":{"id":"f1eb7703"},"outputs":[],"source":["with rc_context({'figure.figsize': (12, 12)}):\n","    sc.pl.umap(adata, color='solo_singlet', size = 30)"]},{"cell_type":"code","execution_count":null,"id":"18fb4f08","metadata":{"id":"18fb4f08"},"outputs":[],"source":["lim= 1"]},{"cell_type":"code","execution_count":null,"id":"91f6034a","metadata":{"id":"91f6034a"},"outputs":[],"source":["adata.obs[adata.obs['solo_doublet'] > lim]"]},{"cell_type":"code","execution_count":null,"id":"a7ad25d8","metadata":{"id":"a7ad25d8"},"outputs":[],"source":["adata.obs['top_doublets'] = 'no'\n","adata.obs.loc[adata.obs['solo_doublet'] > lim, \"top_doublets\"] = \"top_doublet\""]},{"cell_type":"code","execution_count":null,"id":"e76e75ff","metadata":{"id":"e76e75ff"},"outputs":[],"source":["with rc_context({'figure.figsize': (12, 12)}):\n","    sc.pl.umap(adata, color='top_doublets', size = 30)"]}],"metadata":{"kernelspec":{"display_name":"Python 3 (ipykernel)","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.9.12"},"colab":{"provenance":[]}},"nbformat":4,"nbformat_minor":5}