Pristina atlas analysis 1 preprocessing scrublet vs solo.ipynb

{"cells":[{"cell_type":"markdown","id":"72ece39b","metadata":{"id":"72ece39b"},"source":["# Importing modules and settings"]},{"cell_type":"code","execution_count":null,"id":"238c8e41","metadata":{"id":"238c8e41"},"outputs":[],"source":["import numpy as np\n","import pandas as pd\n","import scanpy as sc"]},{"cell_type":"code","execution_count":null,"id":"a6ca374b","metadata":{"id":"a6ca374b"},"outputs":[],"source":["from matplotlib.pyplot import rc_context"]},{"cell_type":"code","execution_count":null,"id":"qJmDcET9-aIl","metadata":{"id":"qJmDcET9-aIl"},"outputs":[],"source":["import seaborn as sns"]},{"cell_type":"code","execution_count":null,"id":"5851f3be","metadata":{"id":"5851f3be"},"outputs":[],"source":["import matplotlib.pyplot as plt"]},{"cell_type":"markdown","id":"4133c199","metadata":{"id":"4133c199"},"source":["General settings of Scanpy"]},{"cell_type":"code","execution_count":null,"id":"3be21d53","metadata":{"id":"3be21d53"},"outputs":[],"source":["sc.settings.verbosity = 4\n","sc.logging.print_header()\n","sc.settings.set_figure_params(dpi=80, facecolor='white')\n"]},{"cell_type":"code","execution_count":null,"id":"uEx2eXdl-ZG4","metadata":{"id":"uEx2eXdl-ZG4"},"outputs":[],"source":["umap_cmap = sns.light_palette('xkcd:medium blue', as_cmap = True)"]},{"cell_type":"markdown","id":"37ab1998","metadata":{"id":"37ab1998"},"source":["# Declaring the input and output files"]},{"cell_type":"code","execution_count":null,"id":"292c5538","metadata":{"id":"292c5538"},"outputs":[],"source":["name_of_analysis = 'pristina_atlas'"]},{"cell_type":"code","execution_count":null,"id":"d90e8a04","metadata":{"id":"d90e8a04"},"outputs":[],"source":["sc.settings.figdir = './figures/'+name_of_analysis+'_doublets_included'"]},{"cell_type":"code","execution_count":null,"id":"39f3c747","metadata":{"id":"39f3c747"},"outputs":[],"source":["results_file_with_doublets = './'+name_of_analysis+'_doublets_included.h5ad'"]},{"cell_type":"code","execution_count":null,"id":"DDWtrVCbZ6Cr","metadata":{"id":"DDWtrVCbZ6Cr"},"outputs":[],"source":["results_file_prefiltering = './'+name_of_analysis+'_prefiltering.h5ad'"]},{"cell_type":"code","execution_count":null,"id":"f742fb8e","metadata":{"id":"f742fb8e"},"outputs":[],"source":["adata = sc.read_10x_mtx(\n","    \"./pristina/\",\n","    var_names='gene_symbols',\n","    cache=True)"]},{"cell_type":"code","execution_count":null,"id":"127586d1","metadata":{"id":"127586d1"},"outputs":[],"source":["adata.var_names_make_unique()"]},{"cell_type":"code","execution_count":null,"id":"0fb8b85b","metadata":{"id":"0fb8b85b"},"outputs":[],"source":["adata.var_names"]},{"cell_type":"code","execution_count":null,"id":"31607fb9","metadata":{"id":"31607fb9"},"outputs":[],"source":["adata.var"]},{"cell_type":"code","execution_count":null,"id":"8cb2aabc","metadata":{"id":"8cb2aabc"},"outputs":[],"source":["adata"]},{"cell_type":"markdown","id":"3f96d73d","metadata":{"id":"3f96d73d"},"source":["# Annotating the samples"]},{"cell_type":"code","execution_count":null,"id":"f34d1587","metadata":{"id":"f34d1587"},"outputs":[],"source":["adata.obs"]},{"cell_type":"code","execution_count":null,"id":"24c1af1e","metadata":{"id":"24c1af1e"},"outputs":[],"source":["sample_ids = adata.obs.index.str.slice(start = 0, stop = -24)"]},{"cell_type":"code","execution_count":null,"id":"19082e96","metadata":{"id":"19082e96"},"outputs":[],"source":["sample_ids"]},{"cell_type":"code","execution_count":null,"id":"102792a3","metadata":{"id":"102792a3"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"199c204a","metadata":{"id":"199c204a"},"outputs":[],"source":["sample_ids_split = sample_ids.str.split(\"_\")"]},{"cell_type":"code","execution_count":null,"id":"2d6e1319","metadata":{"id":"2d6e1319"},"outputs":[],"source":["sample_ids_split"]},{"cell_type":"code","execution_count":null,"id":"b558a119","metadata":{"id":"b558a119"},"outputs":[],"source":["set(sample_ids)"]},{"cell_type":"code","execution_count":null,"id":"062c99dc","metadata":{"id":"062c99dc"},"outputs":[],"source":["list(set(sample_ids))"]},{"cell_type":"code","execution_count":null,"id":"a3f472b0","metadata":{"id":"a3f472b0"},"outputs":[],"source":["experiments = list(set(item[0]+'_'+item[1] for item in sample_ids_split))"]},{"cell_type":"code","execution_count":null,"id":"d8f5b225","metadata":{"id":"d8f5b225"},"outputs":[],"source":["experiments"]},{"cell_type":"code","execution_count":null,"id":"b18f14a3","metadata":{"id":"b18f14a3"},"outputs":[],"source":["libraries = list(set(item[0]+'_'+item[1]+'_'+item[2] for item in sample_ids_split))"]},{"cell_type":"code","execution_count":null,"id":"33229ea4","metadata":{"id":"33229ea4"},"outputs":[],"source":["libraries"]},{"cell_type":"code","execution_count":null,"id":"e41109be","metadata":{"id":"e41109be"},"outputs":[],"source":["for word in experiments:\n","        cellfilt = adata.obs.index.str.contains(word+'_')\n","        adata.obs.loc[cellfilt, \"Experiment\"] = word"]},{"cell_type":"code","execution_count":null,"id":"c8fbc38f","metadata":{"id":"c8fbc38f"},"outputs":[],"source":["for word in libraries:\n","        cellfilt = adata.obs.index.str.contains(word+'_')\n","        adata.obs.loc[cellfilt, \"Library\"] = word"]},{"cell_type":"code","execution_count":null,"id":"3ab4661b","metadata":{"id":"3ab4661b"},"outputs":[],"source":["adata.obs"]},{"cell_type":"code","execution_count":null,"id":"3429b7fa","metadata":{"id":"3429b7fa"},"outputs":[],"source":["adata.obs.iloc[32500]"]},{"cell_type":"markdown","id":"N-614LZIy-W6","metadata":{"id":"N-614LZIy-W6"},"source":["# **Scrublet**"]},{"cell_type":"code","execution_count":null,"id":"f573c047","metadata":{"id":"f573c047","scrolled":true},"outputs":[],"source":["sc.external.pp.scrublet(adata, batch_key = 'Experiment', threshold = 0.14)"]},{"cell_type":"code","execution_count":null,"id":"e5e220ee","metadata":{"id":"e5e220ee"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"05836a54","metadata":{"id":"05836a54"},"outputs":[],"source":["sc.external.pl.scrublet_score_distribution(adata)"]},{"cell_type":"code","execution_count":null,"id":"755b5690","metadata":{"id":"755b5690"},"outputs":[],"source":["adata.obs"]},{"cell_type":"code","execution_count":null,"id":"38183701","metadata":{"id":"38183701"},"outputs":[],"source":["adata.obs['predicted_doublet'].value_counts()"]},{"cell_type":"code","execution_count":null,"id":"frXBISm35mQj","metadata":{"id":"frXBISm35mQj"},"outputs":[],"source":["adata"]},{"cell_type":"code","execution_count":null,"id":"_VEhfRlJ5mTu","metadata":{"id":"_VEhfRlJ5mTu"},"outputs":[],"source":["pd.pivot_table(adata.obs, index = 'predicted_doublet')"]},{"cell_type":"code","execution_count":null,"id":"0jH8uMSF5mWg","metadata":{"id":"0jH8uMSF5mWg"},"outputs":[],"source":[]},{"cell_type":"markdown","id":"9zgO06181kOs","metadata":{"id":"9zgO06181kOs"},"source":["## **Reading SOLO output**"]},{"cell_type":"code","execution_count":null,"id":"by_IHggK1gtl","metadata":{"id":"by_IHggK1gtl"},"outputs":[],"source":["solo = pd.read_excel('./solo_ratio_multimappers 10.xlsx', index_col = 'Unnamed: 0')"]},{"cell_type":"code","execution_count":null,"id":"f6d18a0b","metadata":{"id":"f6d18a0b"},"outputs":[],"source":["solo.index = solo.index.str.slice(stop=-2)"]},{"cell_type":"code","execution_count":null,"id":"hIdQlxZQ1gwT","metadata":{"id":"hIdQlxZQ1gwT"},"outputs":[],"source":["solo"]},{"cell_type":"code","execution_count":null,"id":"b2f16a3c","metadata":{"id":"b2f16a3c"},"outputs":[],"source":["solo['doublet']"]},{"cell_type":"code","execution_count":null,"id":"2LvIEbqC6T8F","metadata":{"id":"2LvIEbqC6T8F"},"outputs":[],"source":["adata.obs['solo_doublet'] = solo['doublet']"]},{"cell_type":"code","execution_count":null,"id":"exl7OksH9QK2","metadata":{"id":"exl7OksH9QK2"},"outputs":[],"source":["adata.obs['solo_singlet'] = solo['singlet']"]},{"cell_type":"code","execution_count":null,"id":"8GZ9Au8F6UAl","metadata":{"id":"8GZ9Au8F6UAl"},"outputs":[],"source":["adata.obs"]},{"cell_type":"code","execution_count":null,"id":"pypJElbv6UDG","metadata":{"id":"pypJElbv6UDG"},"outputs":[],"source":["pd.pivot_table(adata.obs, index = 'predicted_doublet')"]},{"cell_type":"code","execution_count":null,"id":"39qUCapEbcd0","metadata":{"id":"39qUCapEbcd0"},"outputs":[],"source":["th_solo = 1.50"]},{"cell_type":"code","execution_count":null,"id":"ufsbB4xCbMZy","metadata":{"id":"ufsbB4xCbMZy"},"outputs":[],"source":["adata.obs[adata.obs['solo_doublet'] > th_solo]"]},{"cell_type":"code","execution_count":null,"id":"k46rxSwIbMdT","metadata":{"id":"k46rxSwIbMdT"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"vEply9hD-lPe","metadata":{"id":"vEply9hD-lPe"},"outputs":[],"source":["adata.obs['solo_top'] = \"singlet\""]},{"cell_type":"code","execution_count":null,"id":"gikIsZye-sDM","metadata":{"id":"gikIsZye-sDM"},"outputs":[],"source":["adata.obs"]},{"cell_type":"code","execution_count":null,"id":"fbymCZ4vAYz6","metadata":{"id":"fbymCZ4vAYz6"},"outputs":[],"source":["filt_solo_top = adata.obs['solo_doublet'] > th_solo"]},{"cell_type":"code","execution_count":null,"id":"kQnYzGmRAY3P","metadata":{"id":"kQnYzGmRAY3P"},"outputs":[],"source":["adata.obs[filt_solo_top]"]},{"cell_type":"code","execution_count":null,"id":"8CXgNE1UAY6J","metadata":{"id":"8CXgNE1UAY6J"},"outputs":[],"source":["adata.obs.loc[filt_solo_top, 'solo_top'] = 'doublet'"]},{"cell_type":"code","execution_count":null,"id":"TNugZbsSAY9S","metadata":{"id":"TNugZbsSAY9S"},"outputs":[],"source":["adata.obs"]},{"cell_type":"code","execution_count":null,"id":"aQGriclKBSyn","metadata":{"id":"aQGriclKBSyn"},"outputs":[],"source":["adata.obs['solo_top'].value_counts()"]},{"cell_type":"code","execution_count":null,"id":"5YsEIYInBsn1","metadata":{"id":"5YsEIYInBsn1"},"outputs":[],"source":["doub_cols = adata.obs[['predicted_doublet', 'solo_top']]"]},{"cell_type":"code","execution_count":null,"id":"cQ9Iw8uGB_O9","metadata":{"id":"cQ9Iw8uGB_O9"},"outputs":[],"source":["pd.pivot_table(doub_cols, index = 'solo_top')"]},{"cell_type":"code","execution_count":null,"id":"Z0wLW34iCU9v","metadata":{"id":"Z0wLW34iCU9v"},"outputs":[],"source":["filsolo = doub_cols['solo_top'] == 'doublet'"]},{"cell_type":"code","execution_count":null,"id":"tJmK5c0NCl6w","metadata":{"id":"tJmK5c0NCl6w"},"outputs":[],"source":["filscrub = doub_cols['predicted_doublet'] == True"]},{"cell_type":"code","execution_count":null,"id":"N2Ue9EJXC7pn","metadata":{"id":"N2Ue9EJXC7pn"},"outputs":[],"source":["doub_cols[filsolo & filscrub]"]},{"cell_type":"code","execution_count":null,"id":"KoDrehJMC7v2","metadata":{"id":"KoDrehJMC7v2"},"outputs":[],"source":["adata.obs[filsolo & filscrub]"]},{"cell_type":"markdown","id":"7dc1da92","metadata":{"executionInfo":{"elapsed":336,"status":"ok","timestamp":1657361678523,"user":{"displayName":"Jordi Solana","userId":"06184184235792731051"},"user_tz":-60},"id":"7dc1da92"},"source":["# Exporting h5ad without doublets"]},{"cell_type":"code","execution_count":null,"id":"e269ce4e","metadata":{"id":"e269ce4e"},"outputs":[],"source":["adata.obs[~(filsolo | filscrub)]"]},{"cell_type":"code","execution_count":null,"id":"09ce606d","metadata":{"id":"09ce606d"},"outputs":[],"source":["adata.obs"]},{"cell_type":"code","execution_count":null,"id":"8c7b4222","metadata":{"id":"8c7b4222"},"outputs":[],"source":["adata.obs.loc[(adata.obs['predicted_doublet'] == False) & (adata.obs['solo_top'] == 'singlet'), 'doublets'] = 'singlet'"]},{"cell_type":"code","execution_count":null,"id":"2a7a5e2b","metadata":{"id":"2a7a5e2b"},"outputs":[],"source":["adata.obs.loc[(adata.obs['predicted_doublet'] == True) & (adata.obs['solo_top'] == 'singlet'), 'doublets'] = 'doublet scrublet'"]},{"cell_type":"code","execution_count":null,"id":"0b532622","metadata":{"id":"0b532622"},"outputs":[],"source":["adata.obs.loc[(adata.obs['predicted_doublet'] == False) & (adata.obs['solo_top'] == 'doublet'), 'doublets'] = 'doublet solo'"]},{"cell_type":"code","execution_count":null,"id":"a1908483","metadata":{"id":"a1908483"},"outputs":[],"source":["adata.obs.loc[(adata.obs['predicted_doublet'] == True) & (adata.obs['solo_top'] == 'doublet'), 'doublets'] = 'doublet both'"]},{"cell_type":"code","execution_count":null,"id":"ce9a8789","metadata":{"id":"ce9a8789"},"outputs":[],"source":["adata.obs['doublets'] = adata.obs['doublets'].astype('category')"]},{"cell_type":"code","execution_count":null,"id":"96c8ad9b","metadata":{"id":"96c8ad9b"},"outputs":[],"source":["adata.obs['doublets'].cat.reorder_categories(['singlet', 'doublet solo', 'doublet scrublet', 'doublet both'], inplace=True)"]},{"cell_type":"code","execution_count":null,"id":"2cc0d679","metadata":{"id":"2cc0d679"},"outputs":[],"source":["adata.obs['doublets'].value_counts()"]},{"cell_type":"code","execution_count":null,"id":"d208a1f8","metadata":{"id":"d208a1f8"},"outputs":[],"source":["adata[~(filsolo | filscrub)]"]},{"cell_type":"code","execution_count":null,"id":"38189b93","metadata":{"id":"38189b93"},"outputs":[],"source":["adata_no_doublets = adata[~(filsolo | filscrub)]"]},{"cell_type":"code","execution_count":null,"id":"5d88e29b","metadata":{"id":"5d88e29b"},"outputs":[],"source":["adata_no_doublets.write(results_file_prefiltering)"]},{"cell_type":"markdown","id":"eca28d9f","metadata":{"id":"eca28d9f"},"source":["# Preprocessing"]},{"cell_type":"code","execution_count":null,"id":"bbccc3bd","metadata":{"id":"bbccc3bd"},"outputs":[],"source":["sc.pl.highest_expr_genes(adata, n_top=20 )"]},{"cell_type":"code","execution_count":null,"id":"5bb0deb7","metadata":{"id":"5bb0deb7"},"outputs":[],"source":["sc.pp.filter_cells(adata, min_counts=50)\n","sc.pp.filter_cells(adata, min_genes= 50)\n","sc.pp.filter_genes(adata, max_counts = 1000000)"]},{"cell_type":"code","execution_count":null,"id":"d236f397","metadata":{"id":"d236f397"},"outputs":[],"source":["adata.var"]},{"cell_type":"code","execution_count":null,"id":"9a5dbb67","metadata":{"id":"9a5dbb67"},"outputs":[],"source":["sc.pl.highest_expr_genes(adata, n_top=20, )"]},{"cell_type":"code","execution_count":null,"id":"458f1bcd","metadata":{"id":"458f1bcd"},"outputs":[],"source":["adata.var['mt'] = adata.var_names.str.startswith('MT-')  # annotate the group of mitochondrial genes as 'mt'\n","sc.pp.calculate_qc_metrics(adata, qc_vars=['mt'], percent_top=None, log1p=False, inplace=True)"]},{"cell_type":"code","execution_count":null,"id":"684ca625","metadata":{"id":"684ca625"},"outputs":[],"source":["sc.pl.violin(adata, ['n_genes_by_counts', 'total_counts', 'pct_counts_mt'],\n","             jitter=0.4, multi_panel=True, log = True)"]},{"cell_type":"code","execution_count":null,"id":"ecd92371","metadata":{"id":"ecd92371"},"outputs":[],"source":["adata"]},{"cell_type":"markdown","id":"90f07840","metadata":{"id":"90f07840"},"source":["# Matrix slicing"]},{"cell_type":"code","execution_count":null,"id":"b86c5fea","metadata":{"id":"b86c5fea","scrolled":true},"outputs":[],"source":["sc.pl.scatter(adata, x='total_counts', y='n_genes_by_counts')"]},{"cell_type":"code","execution_count":null,"id":"74686eaa","metadata":{"id":"74686eaa"},"outputs":[],"source":["adata = adata[adata.obs.n_genes_by_counts < 700, :]"]},{"cell_type":"code","execution_count":null,"id":"dc9ee576","metadata":{"id":"dc9ee576"},"outputs":[],"source":["adata = adata[adata.obs.total_counts < 900, :]"]},{"cell_type":"code","execution_count":null,"id":"d61c9e7a","metadata":{"id":"d61c9e7a"},"outputs":[],"source":["sc.pl.scatter(adata, x='total_counts', y='n_genes_by_counts')"]},{"cell_type":"markdown","id":"cba76180","metadata":{"id":"cba76180"},"source":["# Normalization and log transformation"]},{"cell_type":"markdown","id":"dcc63620","metadata":{"id":"dcc63620"},"source":["The following 2 functions normalise and log transform the matrix"]},{"cell_type":"code","execution_count":null,"id":"afb05003","metadata":{"id":"afb05003"},"outputs":[],"source":["sc.pp.normalize_total(adata, target_sum=1e4)"]},{"cell_type":"code","execution_count":null,"id":"1888c724","metadata":{"id":"1888c724"},"outputs":[],"source":["sc.pp.log1p(adata)"]},{"cell_type":"markdown","id":"679d9115","metadata":{"id":"679d9115"},"source":["# Selecting highly variable genes"]},{"cell_type":"code","execution_count":null,"id":"88018c6c","metadata":{"id":"88018c6c"},"outputs":[],"source":["sc.pp.highly_variable_genes(adata, n_top_genes = 18000)"]},{"cell_type":"code","execution_count":null,"id":"4ae4f3db","metadata":{"id":"4ae4f3db"},"outputs":[],"source":["sc.pl.highly_variable_genes(adata)"]},{"cell_type":"code","execution_count":null,"id":"05ec9a08","metadata":{"id":"05ec9a08"},"outputs":[],"source":["adata.raw = adata"]},{"cell_type":"code","execution_count":null,"id":"2428ce6e","metadata":{"id":"2428ce6e"},"outputs":[],"source":["adata = adata[:, adata.var.highly_variable]"]},{"cell_type":"code","execution_count":null,"id":"818d0d31","metadata":{"id":"818d0d31"},"outputs":[],"source":["adata"]},{"cell_type":"code","execution_count":null,"id":"fbc16a58","metadata":{"id":"fbc16a58"},"outputs":[],"source":["adata.raw.var"]},{"cell_type":"code","execution_count":null,"id":"7c25920a","metadata":{"id":"7c25920a"},"outputs":[],"source":[]},{"cell_type":"markdown","id":"e4697b64","metadata":{"id":"e4697b64"},"source":["# Scaling the data"]},{"cell_type":"code","execution_count":null,"id":"796ab80b","metadata":{"id":"796ab80b"},"outputs":[],"source":["sc.pp.scale(adata, zero_center=False)"]},{"cell_type":"markdown","id":"3dce232c","metadata":{"id":"3dce232c"},"source":["# Performing the PCA and kNN analysis"]},{"cell_type":"code","execution_count":null,"id":"02f82eae","metadata":{"id":"02f82eae"},"outputs":[],"source":["sc.tl.pca(adata, svd_solver='arpack', n_comps = 150)"]},{"cell_type":"code","execution_count":null,"id":"ca7f59a8","metadata":{"id":"ca7f59a8"},"outputs":[],"source":["sc.pl.pca_variance_ratio(adata, n_pcs=150, log=True)"]},{"cell_type":"code","execution_count":null,"id":"c000970f","metadata":{"id":"c000970f"},"outputs":[],"source":["sc.pp.neighbors(adata, n_neighbors=45, n_pcs=105)"]},{"cell_type":"code","execution_count":null,"id":"04e3a45d","metadata":{"id":"04e3a45d"},"outputs":[],"source":["sc.tl.umap(adata, min_dist=0.5, spread = 1, alpha = 1, gamma = 1.0)"]},{"cell_type":"code","execution_count":null,"id":"26116f26","metadata":{"id":"26116f26"},"outputs":[],"source":["sc.pl.umap(adata)"]},{"cell_type":"code","execution_count":null,"id":"f3afca2c","metadata":{"id":"f3afca2c"},"outputs":[],"source":["tr = 'PrileiEVm023936t1'\n","sc.pl.umap(adata, color=tr, title = tr, color_map = umap_cmap, save = tr+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"be014124","metadata":{"id":"be014124"},"outputs":[],"source":["tr = 'PrileiEVm008309t1'\n","sc.pl.umap(adata, color=tr, title = tr, color_map = umap_cmap, save = tr+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"2b9053e2","metadata":{"id":"2b9053e2"},"outputs":[],"source":["tr = 'PrileiEVm011741t1'\n","sc.pl.umap(adata, color=tr, title = tr, color_map = umap_cmap, save = tr+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"85dbbace","metadata":{"id":"85dbbace"},"outputs":[],"source":["tr = 'PrileiEVm021316t1'\n","sc.pl.umap(adata, color=tr, title = tr, color_map = umap_cmap, save = tr+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"65f61cca","metadata":{"id":"65f61cca"},"outputs":[],"source":["tr = 'PrileiEVm022250t1'\n","sc.pl.umap(adata, color=tr, title = tr, color_map = umap_cmap, save = tr+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"534ad76e","metadata":{"id":"534ad76e"},"outputs":[],"source":["tr = 'PrileiEVm000325t1'\n","sc.pl.umap(adata, color=tr, title = tr, color_map = umap_cmap, save = tr+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"a61d8e32","metadata":{"id":"a61d8e32"},"outputs":[],"source":["tr = 'PrileiEVm013699t1'\n","sc.pl.umap(adata, color=tr, title = tr, color_map = umap_cmap, save = tr+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"094a309a","metadata":{"id":"094a309a"},"outputs":[],"source":["tr = 'PrileiEVm020595t1'\n","sc.pl.umap(adata, color=tr, title = tr, color_map = umap_cmap, save = tr+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"c6ab4008","metadata":{"id":"c6ab4008"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"8e352c18","metadata":{"id":"8e352c18"},"outputs":[],"source":["sc.pl.umap(adata, color='PrileiEVm023936t1', title = 'PrileiEVm023936t1', color_map = umap_cmap)"]},{"cell_type":"code","execution_count":null,"id":"34e392fb","metadata":{"id":"34e392fb"},"outputs":[],"source":["sc.pl.umap(adata, color='PrileiEVm008309t1', title = 'PrileiEVm008309t1', color_map = umap_cmap)"]},{"cell_type":"code","execution_count":null,"id":"7159aad0","metadata":{"id":"7159aad0"},"outputs":[],"source":["sc.pl.umap(adata, color='PrileiEVm021040t1', title = 'PrileiEVm021040t1', color_map = umap_cmap)"]},{"cell_type":"code","execution_count":null,"id":"289a4220","metadata":{"id":"289a4220"},"outputs":[],"source":["sc.pl.umap(adata, color='PrileiEVm017310t1', title = 'PrileiEVm017310t1', color_map = umap_cmap)"]},{"cell_type":"code","execution_count":null,"id":"58940aaf","metadata":{"id":"58940aaf"},"outputs":[],"source":["sc.pl.umap(adata, color='PrileiEVm000199t1', title = 'PrileiEVm000199t1', color_map = umap_cmap)"]},{"cell_type":"code","execution_count":null,"id":"c3105db4","metadata":{"id":"c3105db4"},"outputs":[],"source":["sc.pl.umap(adata, color='PrileiEVm019805t1', title = 'PrileiEVm019805t1', color_map = umap_cmap)"]},{"cell_type":"code","execution_count":null,"id":"e3db3b10","metadata":{"id":"e3db3b10"},"outputs":[],"source":["with rc_context({'figure.figsize': (12, 12)}):\n","    sc.pl.umap(adata, color='doublets', size = 20, groups = ['doublet solo', 'doublet scrublet', 'doublet both'], palette = ['lightgrey', 'pink', 'orange', 'red'],\n","              save = 'doublet.pdf')\n","    "]},{"cell_type":"markdown","id":"4bfb1da3","metadata":{"id":"4bfb1da3"},"source":["# Clustering"]},{"cell_type":"markdown","id":"d8f4b07b","metadata":{"id":"d8f4b07b"},"source":["Indicate how many different resolutions you want to try"]},{"cell_type":"code","execution_count":null,"id":"72770b23","metadata":{"id":"72770b23"},"outputs":[],"source":["resolutions = [1, 2, 3, 4]"]},{"cell_type":"code","execution_count":null,"id":"b8b19cbb","metadata":{"id":"b8b19cbb"},"outputs":[],"source":["for i in resolutions:\n","    sc.tl.leiden(adata, resolution = i, key_added = 'leiden_with_doublet_'+str(i))\n","    sc.pl.umap(adata, color='leiden_with_doublet_'+str(i))"]},{"cell_type":"code","execution_count":null,"id":"802eb466","metadata":{"id":"802eb466"},"outputs":[],"source":["leiden_names = adata.obs.columns[adata.obs.columns.str.contains('leiden')].to_list()"]},{"cell_type":"code","execution_count":null,"id":"72a0f50a","metadata":{"id":"72a0f50a"},"outputs":[],"source":["leiden_names"]},{"cell_type":"code","execution_count":null,"id":"dbBJrcxVd5gc","metadata":{"id":"dbBJrcxVd5gc"},"outputs":[],"source":["clusteringlayer = 'leiden_with_doublet_3'"]},{"cell_type":"code","execution_count":null,"id":"7f367e4f","metadata":{"id":"7f367e4f"},"outputs":[],"source":["sc.pl.umap(adata, color=leiden_names, legend_loc = 'on data', legend_fontsize = 10)"]},{"cell_type":"code","execution_count":null,"id":"159751a9","metadata":{"id":"159751a9"},"outputs":[],"source":["for leiden_i in leiden_names:\n","    with rc_context({'figure.figsize': (25, 25)}):\n","        sc.pl.umap(adata, color=leiden_i, legend_loc='on data', title=str(leiden_i), size = 50, frameon=False,\n","                  save = leiden_i+'.pdf')"]},{"cell_type":"code","execution_count":null,"id":"3aca2fab","metadata":{"id":"3aca2fab"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"ba7d0345","metadata":{"id":"ba7d0345"},"outputs":[],"source":["percs_leiden_1 = {}\n","for cl in adata.obs['leiden_with_doublet_1'].cat.categories:\n","    cts = adata.obs[adata.obs['leiden_with_doublet_1'] == cl]['doublets'].value_counts()\n","    percs = cts / cts.sum() * 100\n","    percs_leiden_1[cl] = percs\n","percs_df_leiden_1 = pd.DataFrame(percs_leiden_1)"]},{"cell_type":"code","execution_count":null,"id":"121be784","metadata":{"id":"121be784"},"outputs":[],"source":["with rc_context({'figure.figsize': (25, 5)}):\n","    percs_df_leiden_1.transpose().plot(kind='bar', stacked=True, color=['lightgrey', 'pink', 'orange', 'red'])\n","    plt.legend(loc='lower right')\n","    plt.savefig('./figures/pristina_atlas_doublets_included/percs_leiden_1.pdf')"]},{"cell_type":"code","execution_count":null,"id":"f3a4e01d","metadata":{"id":"f3a4e01d"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"b26c8009","metadata":{"id":"b26c8009"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"f837019b","metadata":{"id":"f837019b"},"outputs":[],"source":["percs_leiden_2 = {}\n","for cl in adata.obs['leiden_with_doublet_2'].cat.categories:\n","    cts = adata.obs[adata.obs['leiden_with_doublet_2'] == cl]['doublets'].value_counts()\n","    percs = cts / cts.sum() * 100\n","    percs_leiden_2[cl] = percs\n","percs_df_leiden_2 = pd.DataFrame(percs_leiden_2)"]},{"cell_type":"code","execution_count":null,"id":"6989a395","metadata":{"id":"6989a395"},"outputs":[],"source":["with rc_context({'figure.figsize': (25, 5)}):\n","    percs_df_leiden_2.transpose().plot(kind='bar', stacked=True, color=['lightgrey', 'pink', 'orange', 'red'])\n","    plt.legend(loc='lower right')\n","    plt.savefig('./figures/pristina_atlas_doublets_included/percs_leiden_2.pdf')"]},{"cell_type":"code","execution_count":null,"id":"25355976","metadata":{"id":"25355976"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"42c22516","metadata":{"id":"42c22516"},"outputs":[],"source":["percs_leiden_3 = {}\n","for cl in adata.obs['leiden_with_doublet_3'].cat.categories:\n","    cts = adata.obs[adata.obs['leiden_with_doublet_3'] == cl]['doublets'].value_counts()\n","    percs = cts / cts.sum() * 100\n","    percs_leiden_3[cl] = percs\n","percs_df_leiden_3 = pd.DataFrame(percs_leiden_3)"]},{"cell_type":"code","execution_count":null,"id":"d89cb850","metadata":{"id":"d89cb850"},"outputs":[],"source":["with rc_context({'figure.figsize': (25, 5)}):\n","    percs_df_leiden_3.transpose().plot(kind='bar', stacked=True, color=['lightgrey', 'pink', 'orange', 'red'])\n","    plt.legend(loc='lower right')\n","    plt.savefig('./figures/pristina_atlas_doublets_included/percs_leiden_3.pdf')"]},{"cell_type":"code","execution_count":null,"id":"2c3ef058","metadata":{"id":"2c3ef058"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"c150d44e","metadata":{"id":"c150d44e"},"outputs":[],"source":["percs_leiden_4 = {}\n","for cl in adata.obs['leiden_with_doublet_4'].cat.categories:\n","    cts = adata.obs[adata.obs['leiden_with_doublet_4'] == cl]['doublets'].value_counts()\n","    percs = cts / cts.sum() * 100\n","    percs_leiden_4[cl] = percs\n","percs_df_leiden_4 = pd.DataFrame(percs_leiden_4)"]},{"cell_type":"code","execution_count":null,"id":"c36fd82a","metadata":{"id":"c36fd82a"},"outputs":[],"source":["with rc_context({'figure.figsize': (25, 5)}):\n","    percs_df_leiden_4.transpose().plot(kind='bar', stacked=True, color=['lightgrey', 'pink', 'orange', 'red'])\n","    plt.legend(loc='lower right')\n","    plt.savefig('./figures/pristina_atlas_doublets_included/percs_leiden_4.pdf')"]},{"cell_type":"code","execution_count":null,"id":"774ff402","metadata":{"id":"774ff402"},"outputs":[],"source":["adata.write(results_file_with_doublets)"]},{"cell_type":"code","execution_count":null,"id":"17a42da7","metadata":{"id":"17a42da7"},"outputs":[],"source":[]}],"metadata":{"colab":{"provenance":[]},"kernelspec":{"display_name":"Python 3","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":"3.8.8"}},"nbformat":4,"nbformat_minor":5}