Upload app.py

app.py

@@ -7,28 +7,25 @@ import scanpy as sc
 
 #import mpld3
 import matplotlib.pyplot as plt
-#import seaborn as sns
 
+#from mpl_toolkits.axes_grid1 import make_axes_locatable
 
-#import streamlit.components.v1 as components
+#import matplotlib.gridspec as gridspec
 
-#from IPython.display import Markdown as md
+#from sunbird.categorical_encoding import frequency_encoding
 
-from functions import pathway_analyses
 
-# SMALL_SIZE = 2
-# MEDIUM_SIZE = 2
-# BIGGER_SIZE = 2
+import seaborn as sns
+
+plt.rcParams.update({'figure.autolayout': True})
+plt.rcParams['axes.linewidth'] = 0.0001
+
+
+from functions import pathway_analyses
 
-# plt.rc('font', size=SMALL_SIZE)          # controls default text sizes
-# plt.rc('axes', titlesize=SMALL_SIZE)     # fontsize of the axes title
-# plt.rc('axes', labelsize=MEDIUM_SIZE)    # fontsize of the x and y labels
-# plt.rc('xtick', labelsize=SMALL_SIZE)    # fontsize of the tick labels
-# plt.rc('ytick', labelsize=SMALL_SIZE)    # fontsize of the tick labels
-# plt.rc('legend', fontsize=SMALL_SIZE)    # legend fontsize
-# plt.rc('figure', titlesize=BIGGER_SIZE)  # fontsize of the figure title
 
-sc.settings.set_figure_params(dpi=80, facecolor='white')
+#sc.settings.set_figure_params(dpi=80, facecolor='white',fontsize=4)
+sc.settings.set_figure_params(dpi=80, facecolor='white',fontsize=12)
 
 #disable st.pyplot warning
 st.set_page_config(layout="wide") 
@@ -83,16 +80,6 @@ def get_data():
     if 'go_table' not in st.session_state:        
         bp = pathway_analyses.read_pathways('pathway_databases/GO_Biological_Process_2021.txt')
 
-        # cy = pathway_analyses.read_pathways('pathway_databases/HumanCyc_2016.txt')
-        # ke = pathway_analyses.read_pathways('pathway_databases/KEGG_2019_Human.txt')
-        # re = pathway_analyses.read_pathways('pathway_databases/Reactome_2016.txt')
-
-        # all_paths = pd.concat([bp, cy, ke, re], join='outer', axis=0, ignore_index=True)
-        # all_paths.set_index(0, inplace=True)
-        # all_paths.fillna("", inplace=True)
-        # all_paths_dict = all_paths.to_dict(orient='index')
-
-
         go_bp_paths = bp.set_index(0)
         go_bp_paths.fillna("", inplace=True)
         go_bp_paths_dict = go_bp_paths.to_dict(orient='index')
@@ -128,21 +115,10 @@ with tab1:
             'Please select CellType',
             st.session_state['cell_type']
             )
-        # with c3:
-        #     plot_choice = st.checkbox(
-        #     "Which Plots",
-        #     ('Gene','Old/Young'))
-            
-            
-
         Updated=st.form_submit_button(label = 'Go')
     if not isinstance(selected_gene, type(None)) and not isinstance(selected_celltype, type(None)) and Updated:
-
-
-        # fig11, axx1 = plt.subplots()
-        # sc.pl.umap(st.session_state['adata_annot'], color='new_anno', title='', legend_loc='on data',legend_fontsize='4', frameon=False,show=False, ax=axx1)
-        # st.pyplot(plt.gcf().set_size_inches(4, 4))     
-
+        fig = plt.figure(figsize=(6, 6))
+        
         col1,col2= st.columns([1,1])
         with col1:
             fig11, axx11 = plt.subplots(figsize=(5,5))
@@ -152,8 +128,11 @@ with tab1:
         with col2:
             fig12, axx12 = plt.subplots(figsize=(5,5))
             #sc.pl.umap(st.session_state['adata_annot'], color='new_anno', title='', legend_loc='on data', frameon=False,show=False, ax=axx2)
-            sc.pl.umap(st.session_state['adata_annot'], color=selected_gene, title=selected_gene, legend_loc='best', frameon=False,show=False,legend_fontsize='xx-small', ax=axx12)#,vmax='p99')
+            sc.pl.umap(st.session_state['adata_annot'], color=selected_gene, title='', legend_loc='best', frameon=False,show=False,legend_fontsize='xx-small', ax=axx12)#,vmax='p99')
             #plt.xticks(rotation = 45)
+            #plt.colorbar(cax=cax)
+            axx12.set_title(selected_gene, fontsize=12)
+            
             st.pyplot(fig12)        
 
         #Subset Younv and Old
@@ -170,83 +149,42 @@ with tab1:
         
         #Young
         dot_size=.05
-        col1,col2= st.columns([1,1])
+        font_sz=4
+        fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(nrows=2, ncols=2,figsize=(3,3))
+        #plt.subplots_adjust(wspace=0, hspace=0)
+        #plt.tight_layout()
+        #fig.tight_layout(rect=[0, 0.03, 1, 0.95]) #[left, bottom, right, top]
+        sc.pl.umap(adata_Young, color=selected_gene, title="", legend_loc='right margin', color_map='viridis',frameon=True,show=False,size=dot_size, legend_fontsize='xx-small',colorbar_loc=None,ax=ax1)  
+        ax1.set_title('All', fontsize=font_sz)
+        ax1.set_ylabel('Young', fontsize=font_sz)
+        #ax1.set_xlabel('', fontsize=0)
+        ax1.get_xaxis().set_visible(False)
+        sc.pl.umap(adata_YoungAst, color=selected_gene, title="", legend_loc='right margin', color_map='viridis', frameon=True,show=False,size=dot_size,legend_fontsize='xx-small',colorbar_loc=None, ax=ax2)  
+        ax2.set_title(selected_celltype, fontsize=font_sz)
+        #ax2.set_xlabel('', fontsize=0)
+        ax2.set_ylabel('', fontsize=0)
+        ax2.get_xaxis().set_visible(False)
+        ax2.get_yaxis().set_visible(False)
+        sc.pl.umap(adata_Old, color=selected_gene, title="", legend_loc='right margin', color_map='viridis', frameon=True,show=False,size=dot_size,legend_fontsize='xx-small', colorbar_loc="bottom",ax=ax3)  
         
-        with col1:
-            
-            #st.markdown('<div style="text-align: center;">**Young**</div>', unsafe_allow_html=True)
-            str_title='Young: '+selected_gene
-            #st.markdown("<h3 style='text-align: center; color: red;'>str_title</h3>", unsafe_allow_html=True)
-            st.markdown("# {} ".format(str_title))#,align_text='center')
-            #md("# {} ".format(str_title))
-
-            fig21, axx21 = plt.subplots(figsize=(1,1))
-            #sc.pl.umap(adata_Young, color=selected_gene, title="Young: "+selected_gene, legend_loc='right margin', color_map='viridis',frameon=False,show=False,size=dot_size, legend_fontsize='4',colorbar_loc=None,ax=axx21)  
-            sc.pl.umap(adata_Young, color=selected_gene, title="", legend_loc='right margin', color_map='viridis',frameon=False,show=False,size=dot_size, legend_fontsize='xx-small',colorbar_loc=None,ax=axx21)  
-            #st.pyplot(fig21)  
-            st.pyplot(plt.gcf())        
-        with col2:
-            str_title='Young: '+selected_gene+" ("+selected_celltype+")"
-            st.markdown("# {} ".format(str_title))#,align_text='center')
-            fig22, axx22 = plt.subplots(figsize=(1,1))
-            #sc.pl.umap(st.session_state['adata_annot'], color='new_anno', title='', legend_loc='on data', frameon=False,show=False, ax=axx2)
-            #sc.pl.umap(st.session_state['adata_annot'], color=selected_gene, title=selected_gene, legend_loc='best', frameon=False,show=False, ax=axx2)#,vmax='p99')
-            sc.pl.umap(adata_YoungAst, color=selected_gene, title="", legend_loc='right margin', color_map='viridis', frameon=False,show=False,size=dot_size,legend_fontsize='xx-small',colorbar_loc=None, ax=axx22)  
-            #sc.pl.umap(adata_Old, color=selected_gene, title="Old: "+selected_gene, legend_loc='right margin', color_map='viridis', frameon=False,show=False, ax=axx22)  
-            #plt.xticks(rotation = 45)
-            #st.pyplot(fig22)        
-            st.pyplot(plt.gcf())  
-        #Old
-        col1,col2= st.columns([1,1])
-        with col1:
-            str_title='Old: '+selected_gene+" ("+selected_celltype+")"
-            st.markdown("# {} ".format(str_title))#,align_text='center')
-            
-            fig31, axx31 = plt.subplots(figsize=(1,1))
-            #sc.pl.umap(st.session_state['adata_annot'], color='new_anno', title='', legend_loc='on data',legend_fontsize='8', frameon=False,show=False, ax=axx1)
-            sc.pl.umap(adata_Old, color=selected_gene, title="", legend_loc='right margin', color_map='viridis', frameon=False,show=False,size=dot_size,legend_fontsize='xx-small', colorbar_loc="bottom",ax=axx31)  
-            st.pyplot(fig31)        
-        with col2:
-            str_title='Old: '+selected_gene+" ("+selected_celltype+")"
-            st.markdown("# {} ".format(str_title))#,align_text='center')
-            
-            fig32, axx32 = plt.subplots(figsize=(1,1))
-            #sc.pl.umap(st.session_state['adata_annot'], color='new_anno', title='', legend_loc='on data', frameon=False,show=False, ax=axx2)
-            #sc.pl.umap(st.session_state['adata_annot'], color=selected_gene, title=selected_gene, legend_loc='best', frameon=False,show=False, ax=axx2)#,vmax='p99')
-            sc.pl.umap(adata_OldAst, color=selected_gene, title="", legend_loc='right margin', color_map='viridis', frameon=False,show=False,size=dot_size,legend_fontsize='xx-small', colorbar_loc="bottom",ax=axx32)  
-            #plt.xticks(rotation = 45)
-            st.pyplot(fig32)        
-        
-        # fig, ax = plt.subplots(3,2)
-        # sc.pl.umap(st.session_state['adata_annot'], color='new_anno', title='', legend_loc='on data', frameon=False,show=False, ax=ax[0,0])
-        # sc.pl.umap(st.session_state['adata_annot'], color=selected_gene, title=selected_gene, legend_loc='best', frameon=False,show=False, ax=ax[0,1],vmax='p99')
-        
-        # #Subset Younv and Old
-        # adata_Young = st.session_state['adata_annot'][st.session_state['adata_annot'].obs['Age_group']=='young']
-        # adata_Old = st.session_state['adata_annot'][st.session_state['adata_annot'].obs['Age_group']=='old']
-        # sc.pl.umap(adata_Young, color=selected_gene, title="Young: "+selected_gene, legend_loc='right margin', color_map='viridis',frameon=False,show=False, ax=ax[1,0])  
-        # sc.pl.umap(adata_Old, color=selected_gene, title="Old: "+selected_gene, legend_loc='right margin', color_map='viridis', frameon=False,show=False, ax=ax[2,0])  
-        
-        # # #Young/Old  but for cell_type
-        # # adata_YoungAst = adata_Young[adata_Young.obs['broad_celltype']==selected_celltype]
-        # # adata_OldAst = adata_Old[adata_Old.obs['broad_celltype']==selected_celltype]
-
-        # #Young/Old  but for cell_type
-        # adata_YoungAst = adata_Young[adata_Young.obs['new_anno']==selected_celltype]
-        # adata_OldAst = adata_Old[adata_Old.obs['new_anno']==selected_celltype]
-        
-        
-        # sc.pl.umap(adata_YoungAst, color=selected_gene, title=selected_celltype, legend_loc='right margin', color_map='viridis', frameon=False,show=False, ax=ax[1,1])  
-        # sc.pl.umap(adata_OldAst, color=selected_gene, title=selected_celltype, legend_loc='right margin', color_map='viridis', frameon=False,show=False, ax=ax[2,1])  
-        
-        # #sc.pl.umap(st.session_state['adata_annot'], color='Brain_region', title='Brain Region', legend_loc='right margin', frameon=False,show=False, ax=ax[1,1])  
-        # #sc.pl.umap(st.session_state['adata_annot'], color='Age_group', title='Age Group', legend_loc='right margin', frameon=False,show=False, ax=ax[2,0])  
-        # #sc.pl.umap(st.session_state['adata_annot'], color=selected_celltype, title=selected_celltype, legend_loc='on data', frameon=False,show=False, ax=ax[2,1])  
+        #ax3.set_xlabel('x-label', fontsize=12)
+        ax3.set_ylabel('Old', fontsize=font_sz)
+        #ax3.set_xlabel('', fontsize=0)
+        ax3.get_xaxis().set_visible(False)
+        #ax3.get_title().set_visible(False)
+        sc.pl.umap(adata_OldAst, color=selected_gene, title="", legend_loc='right margin', color_map='viridis', frameon=True,show=False,size=dot_size,legend_fontsize='xx-small', colorbar_loc="bottom",ax=ax4)  
+        #ax4.set_xlabel('', fontsize=0)
+        #ax4.set_ylabel('', fontsize=0)
+        ax4.get_xaxis().set_visible(False)
+        ax4.get_yaxis().set_visible(False)
+        #ax4.get_title().set_visible(False)
+        plt.suptitle(selected_gene+"\ncoefficient estimate: 0.24 | BH-FDR p=7.91x$10^{-3}$",fontsize=font_sz)
         
+        #plt.subplots_adjust(top=0.95)
         
-        # st.pyplot(plt.gcf().set_size_inches(15, 30))
-                
-
+        #plt.tight_layout(pad=0, w_pad=0, h_pad=0)
+        #plt.tight_layout()
+        st.pyplot(plt.gcf())        
 
 with tab2:
     with st.form(key='multiselect_form'):
@@ -271,25 +209,19 @@ with tab2:
         else:
             multi_genes=st.session_state['go_table'].loc[:,go_term]
             multi_genes=multi_genes.dropna().values
+            multi_genes=np.sort(multi_genes)
         #multi_genes=['WNT3', 'VPS13C', 'VAMP4', 'UBTF', 'UBAP2', 'TMEM175', 'TMEM163', 'SYT17', 'STK39', 'SPPL2B', 'SIPA1L2', 'SH3GL2', 'SCARB2', 'SCAF11', 'RPS6KL1', 'RPS12', 'RIT2', 'RIMS1', 'RETREG3', 'PMVK', 'PAM', 'NOD2', 'MIPOL1', 'MEX3C', 'MED12L', 'MCCC1', 'MBNL2', 'MAPT', 'LRRK2', 'KRTCAP2', 'KCNS3', 'KCNIP3', 'ITGA8', 'IP6K2', 'GPNMB', 'GCH1', 'GBA', 'FYN', 'FCGR2A', 'FBRSL1', 'FAM49B', 'FAM171A2', 'ELOVL7', 'DYRK1A', 'DNAH17', 'DLG2', 'CTSB', 'CRLS1', 'CRHR1', 'CLCN3', 'CHRNB1', 'CAMK2D', 'CAB39L', 'BRIP1', 'BIN3', 'ASXL3', 'SNCA']
         #########
-        
-        #sns.clustermap(st.session_state['adata_annot'], figsize=(14,12),
-         #      pivot_kws={'index': 'country', 
-          #                        'columns': 'year',
-           #                       'values': 'lifeExp'})
-        # col1,col2= st.columns([1,1])
-        # #fig_szx=2*len(st.session_state['cell_type'])
-        # #fig_szy=100*len(multi_genes)
-        # with col1:
-        #     figa, axxaa = plt.subplots(figsize=(5, 5))
-        #     #sc.pl.umap(st.session_state['adata_annot'], color='new_anno', title='', legend_loc='on data',legend_fontsize='8', frameon=False,show=False, ax=axx11)
-        #     axxaa=sc.pl.clustermap(st.session_state['adata_annot'], obs_keys=multi_genes) #,'new_anno',size_title='Fraction of\n Expressing Cells',colorbar_title='Mean\nExpression',cmap='BuPu',swap_axes=True,show=False,vmax=5)
-        #     #st.pyplot(fig11)      
-        #     #st.pyplot(plt.gcf().set_size_inches(fig_szx, fig_szy))  
-        #     st.pyplot(plt.gcf())  
-        
-        
+        figxx = plt.subplots(figsize=(5, 5))
+        hmpdat=st.session_state['adata_annot'][:, multi_genes] #.to_df()
+        #st.write(hmpdat)
+        samples=hmpdat.obs.new_anno
+        dfh = pd.DataFrame(hmpdat.X.toarray(), columns = multi_genes)
+        dfh=dfh.T
+        dfh.columns=samples.values.to_list()
+        sns.clustermap(dfh)
+        st.pyplot(plt.gcf())  
+        ######
         
         col1,col2= st.columns([1,1])
         #fig_szx=2*len(st.session_state['cell_type'])
@@ -303,9 +235,11 @@ with tab2:
             st.pyplot(plt.gcf())  
         with col2:
             fig12, axx12 = plt.subplots(figsize=(5, 5))
+            
             #sc.pl.umap(st.session_state['adata_annot'], color='new_anno', title='', legend_loc='on data', frameon=False,show=False, ax=axx2)
             #sc.pl.umap(st.session_state['adata_annot'], color=selected_gene, title=selected_gene, legend_loc='best', frameon=False,show=False,legend_fontsize='xx-small', ax=axx12)#,vmax='p99')
-            axx12=sc.pl.heatmap(st.session_state['adata_annot'], multi_genes, groupby='new_anno', vmin=-1, vmax=1, cmap='BuPu', dendrogram=True, swap_axes=True)#,ax=ax2)
+            axx12=sc.pl.heatmap(st.session_state['adata_annot'], multi_genes, groupby='new_anno', vmin=-1, vmax=1, cmap='BuPu', dendrogram=True, swap_axes=True,var_group_rotation="45")#,ax=ax2)
+            plt.xticks(rotation = 45)
             #plt.xticks(rotation = 45)
             #st.pyplot(fig12)      
             #st.pyplot(plt.gcf().set_size_inches(fig_szx, fig_szy))