Pristina atlas analysis 2 parameter space.ipynb

{"cells":[{"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":"XLpBEAU9_FLQ","metadata":{"id":"XLpBEAU9_FLQ"},"outputs":[],"source":["import seaborn as sns"]},{"cell_type":"code","execution_count":null,"id":"f35e8ce2","metadata":{"id":"f35e8ce2"},"outputs":[],"source":["import matplotlib.pyplot as plt"]},{"cell_type":"code","execution_count":null,"id":"085a588e","metadata":{"id":"085a588e"},"outputs":[],"source":["import os"]},{"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')"]},{"cell_type":"code","execution_count":null,"id":"392d54f5","metadata":{"id":"392d54f5"},"outputs":[],"source":["stepcount = 3"]},{"cell_type":"code","execution_count":null,"id":"4uQt1_P__NAw","metadata":{"id":"4uQt1_P__NAw"},"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":"8c544734","metadata":{"id":"8c544734"},"outputs":[],"source":["sc.settings.figdir = './figures/'+name_of_analysis+'_parameter_space'"]},{"cell_type":"code","execution_count":null,"id":"921bd456","metadata":{"id":"921bd456"},"outputs":[],"source":["adata = sc.read_h5ad('./'+name_of_analysis+'_prefiltering.h5ad')"]},{"cell_type":"code","execution_count":null,"id":"8cb2aabc","metadata":{"id":"8cb2aabc"},"outputs":[],"source":["adata"]},{"cell_type":"code","execution_count":null,"id":"686457de","metadata":{"id":"686457de"},"outputs":[],"source":["adata_unprocessed = adata.copy()"]},{"cell_type":"code","execution_count":null,"id":"5a0e0b33","metadata":{"id":"5a0e0b33"},"outputs":[],"source":["def process(minimum_genes_counts, slice_ngenes, slice_ncounts, n_top, k_neighb, princ_comps, res):\n","    \n","    adata = adata_unprocessed.copy()\n","    sc.pl.highest_expr_genes(adata, n_top=20)\n","    sc.pp.filter_cells(adata, min_counts= minimum_genes_counts) # minimum_genes_counts affect both\n","    sc.pp.filter_cells(adata, min_genes= minimum_genes_counts) # minimum_genes_counts affect both\n","    sc.pp.filter_genes(adata, max_counts = 1000000)\n","    sc.pl.highest_expr_genes(adata, n_top=20, show = False)\n","    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)\n","    sc.pl.scatter(adata, x='total_counts', y='n_genes_by_counts')\n","    adata = adata[adata.obs.n_genes_by_counts < slice_ngenes, :] #slice_ngenes\n","    adata = adata[adata.obs.total_counts < slice_ncounts, :] #slice_ncounts\n","    sc.pl.scatter(adata, x='total_counts', y='n_genes_by_counts')\n","    sc.pp.normalize_total(adata, target_sum=1e4)\n","    sc.pp.log1p(adata)\n","    sc.pp.highly_variable_genes(adata, n_top_genes = n_top) #n_top\n","    sc.pl.highly_variable_genes(adata)\n","    adata.raw = adata\n","    adata = adata[:, adata.var.highly_variable]\n","    sc.pp.scale(adata, zero_center=False)\n","    sc.tl.pca(adata, svd_solver='arpack', n_comps = 150)\n","    sc.pp.neighbors(adata, n_neighbors= k_neighb, n_pcs= princ_comps) #k_neighb, #princ_comps\n","    sc.tl.umap(adata, min_dist=0.5, spread = 1, alpha = 1, gamma = 1.0) \n","    sc.tl.leiden(adata, resolution = res) #res\n"," \n","    fig, axs = plt.subplots(1, 9, figsize = (50, 5))\n","  \n","   \n","    gene0 = 'PrileiEVm023936t1'\n","    gene1 = 'PrileiEVm008309t1'\n","    gene2 = 'PrileiEVm011741t1'\n","    gene3 = 'PrileiEVm021316t1'\n","    gene4 = 'PrileiEVm022250t1'\n","    gene5 = 'PrileiEVm000325t1'\n","    gene6 = 'PrileiEVm013699t1'\n","    gene7 = 'PrileiEVm020595t1'\n","    \n","    sc.pl.umap(adata, color= gene0, title = gene0, color_map = umap_cmap, show = False, ax = axs[0])\n","    sc.pl.umap(adata, color= gene1, title = gene1, color_map = umap_cmap, show = False, ax = axs[1])\n","    sc.pl.umap(adata, color= gene2, title = gene2, color_map = umap_cmap, show = False, ax = axs[2])\n","    sc.pl.umap(adata, color= gene3, title = gene3, color_map = umap_cmap, show = False, ax = axs[3])\n","    sc.pl.umap(adata, color= gene4, title = gene4, color_map = umap_cmap, show = False, ax = axs[4])\n","    sc.pl.umap(adata, color= gene5, title = gene5, color_map = umap_cmap, show = False, ax = axs[5])\n","    sc.pl.umap(adata, color= gene6, title = gene6, color_map = umap_cmap, show = False, ax = axs[6])\n","    sc.pl.umap(adata, color= gene7, title = gene7, color_map = umap_cmap, show = False, ax = axs[7])\n","\n","    n_of_cl = len(adata.obs['leiden'].cat.categories)\n","    sc.pl.umap(adata, color= 'leiden', legend_loc = 'on data', legend_fontsize = 7, title = str(n_of_cl)+' clusters', show = False, ax = axs[8])\n","    return fig"]},{"cell_type":"code","execution_count":null,"id":"02057916","metadata":{"id":"02057916"},"outputs":[],"source":["mynewfig = process(50, 700, 900, 18000, 45, 105, 1)"]},{"cell_type":"code","execution_count":null,"id":"841c60c0","metadata":{"id":"841c60c0"},"outputs":[],"source":["os.mkdir('./figures/pristina_atlas_parameter_space')"]},{"cell_type":"code","execution_count":null,"id":"025aa35f","metadata":{"id":"025aa35f"},"outputs":[],"source":["mynewfig"]},{"cell_type":"code","execution_count":null,"id":"1d96c9f7","metadata":{"id":"1d96c9f7"},"outputs":[],"source":["mynewfig.savefig('./figures/pristina_atlas_parameter_space/figure.pdf', format = 'pdf')"]},{"cell_type":"markdown","id":"4cf075f8","metadata":{"id":"4cf075f8"},"source":["# Parameter space exploration"]},{"cell_type":"code","execution_count":null,"id":"8a92827a","metadata":{"id":"8a92827a"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"NP9TN1iWfwx6","metadata":{"id":"NP9TN1iWfwx6"},"outputs":[],"source":["step = \"minimum_genes_counts\"\n","values_to_try = [30, 40, 50, 60, 70, 80, 90, 100]\n","stepcount += 1\n","os.mkdir('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step)\n","for value in values_to_try:\n","    newfig = process(value, 700, 900, 16000, 45, 95, 1)\n","    newfig.savefig('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step+'/'+str(stepcount)+'_'+step+'_'+str(value)+'.pdf', format = 'pdf')"]},{"cell_type":"code","execution_count":null,"id":"46b7986f","metadata":{"id":"46b7986f"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"0704f361","metadata":{"id":"0704f361"},"outputs":[],"source":["step = \"slice_ngenes\"\n","values_to_try = [300, 400, 500, 600, 700, 800, 900, 1000]\n","stepcount += 1\n","os.mkdir('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step)\n","for value in values_to_try:\n","    newfig = process(50, value, 900, 16000, 45, 95, 1)\n","    newfig.savefig('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step+'/'+str(stepcount)+'_'+step+'_'+str(value)+'.pdf', format = 'pdf')"]},{"cell_type":"code","execution_count":null,"id":"b0b2c10f","metadata":{"id":"b0b2c10f"},"outputs":[],"source":["step = \"slice_ncounts\"\n","values_to_try = [500, 600, 700, 800, 900, 1000, 1100, 1200]\n","stepcount += 1\n","os.mkdir('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step)\n","for value in values_to_try:\n","    newfig = process(50, 700, value, 16000, 45, 95, 1)\n","    newfig.savefig('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step+'/'+str(stepcount)+'_'+step+'_'+str(value)+'.pdf', format = 'pdf')"]},{"cell_type":"code","execution_count":null,"id":"5aca67ec","metadata":{"id":"5aca67ec"},"outputs":[],"source":["step = \"n_top\"\n","values_to_try = [4000, 6000, 8000, 10000, 12000, 14000, 18000, 22000]\n","stepcount += 1\n","os.mkdir('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step)\n","for value in values_to_try:\n","    newfig = process(50, 700, 900, value, 45, 95, 1)\n","    newfig.savefig('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step+'/'+str(stepcount)+'_'+step+'_'+str(value)+'.pdf', format = 'pdf')"]},{"cell_type":"code","execution_count":null,"id":"27b95f3f","metadata":{"id":"27b95f3f"},"outputs":[],"source":["step = \"k_neighb\"\n","values_to_try = [15, 25, 35, 45, 55, 65, 75, 85]\n","stepcount += 1\n","os.mkdir('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step)\n","for value in values_to_try:\n","    newfig = process(50, 700, 900, 18000, value, 95, 1)\n","    newfig.savefig('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step+'/'+str(stepcount)+'_'+step+'_'+str(value)+'.pdf', format = 'pdf')"]},{"cell_type":"code","execution_count":null,"id":"78871b29","metadata":{"id":"78871b29"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"id":"9b388fcc","metadata":{"id":"9b388fcc"},"outputs":[],"source":["step = \"princ_comps\"\n","values_to_try = [15, 25, 45, 65, 85, 105, 125, 145]\n","stepcount += 1\n","os.mkdir('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step)\n","for value in values_to_try:\n","    newfig = process(50, 700, 900, 18000, 45, value, 1)\n","    newfig.savefig('./figures/pristina_atlas_parameter_space/'+str(stepcount)+'_'+step+'/'+str(stepcount)+'_'+step+'_'+str(value)+'.pdf', format = 'pdf')"]},{"cell_type":"code","execution_count":null,"id":"5e8c5d16","metadata":{"id":"5e8c5d16"},"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}