part3_Automatic_Cluster_Annotation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We use SCSA to help annotate the clusters. SCSA annotation is based on a few manually curated database. Instructions can be found https://github.com/bioinfo-ibms-pumc/SCSA."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd /SCSA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DB load: 47347 3 3 48257 37440\n",
      "Namespace(Gensymbol=True, MarkerDB=None, celltype='normal', cluster='all', db='whole.db', foldchange=1.5, input='/scratch/umap_cluster.csv', list_tissue=False, noprint=False, norefdb=False, outfmt='txt', output='/scratch/umap_annotation_result', pvalue=0.01, source='scanpy', species='Human', target='cellmarker', tissue='All', weight=100.0)\n",
      "DB load: 47347 3 3 48257 37440\n",
      "load markers: 45409\n",
      "############################## Cluster 0 ##############################\n",
      "\n",
      "!WARNING3:Zero marker sets found, type:marker\n",
      "!WARNING3:Change the threshold or tissue name and try again?\n",
      "!WARNING3:EnsemblID or GeneID,try '-E' command?\n",
      "Cluster 0 Gene number: 1\n",
      "None\n",
      "Go Enrichment analysis: Group1: 1 Group2: 433\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig             go_name\n",
      " GO:0005507         1              1  0.004608  0.004608  **  copper ion binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                   go_name\n",
      " GO:0005604         1              1  0.004608  0.017281   *                         basement membrane\n",
      " GO:0001669         1              2  0.006912  0.017281   *                         acrosomal vesicle\n",
      " GO:0062023         1             15  0.036866  0.061444   -  collagen-containing extracellular matrix\n",
      " GO:0005615         1             68  0.158986  0.198733   -                       extracellular space\n",
      " GO:0005576         1             87  0.202765  0.202765   -                      extracellular region\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                         go_name\n",
      " GO:0035904         1              1  0.004608  0.013825   *               aorta development\n",
      " GO:0032496         1              4  0.011521  0.017281   *  response to lipopolysaccharide\n",
      " GO:0055114         1             10  0.025346  0.025346   *     oxidation-reduction process\n",
      "\n",
      "Other Gene number: 433\n",
      "############################## Cluster 1 ##############################\n",
      "\n",
      "Cell Num: 59\n",
      "Gene Num: 18\n",
      "Not Zero: 102\n",
      "Cluster 1 Gene number: 22\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?                  Naive T cell         4.5204    1.5  \n",
      "------------------------------------------------------------\n",
      "             (Central memory T cell)   (3.0610)\n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 18 Group2: 423\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                       go_name\n",
      " GO:0005509         3             16  0.036733  0.332844   -           calcium ion binding\n",
      " GO:0003682         2              7  0.047829  0.332844   -             chromatin binding\n",
      " GO:0044325         2              8  0.058349  0.332844   -           ion channel binding\n",
      " GO:1901707         1              1  0.080056  0.332844   -          leptomycin B binding\n",
      " GO:0008092         1              1  0.080056  0.332844   -  cytoskeletal protein binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                 go_name\n",
      " GO:0042383         2              1  0.004616  0.147713   -              sarcolemma\n",
      " GO:0030315         2              1  0.004616  0.147713   -                T-tubule\n",
      " GO:0014704         2              2  0.009008  0.192172   -       intercalated disc\n",
      " GO:0005575         2              4  0.021443  0.343087   -      cellular_component\n",
      " GO:0016324         2              5  0.029295  0.365111   -  apical plasma membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                 go_name\n",
      " GO:0034394         2              2  0.009008  0.231668   -    protein localization to cell surface\n",
      " GO:0043392         2              3  0.014650  0.231668   -      negative regulation of DNA binding\n",
      " GO:0060326         2              3  0.014650  0.231668   -                         cell chemotaxis\n",
      " GO:0007417         2              4  0.021443  0.231668   -      central nervous system development\n",
      " GO:0071345         2              5  0.029295  0.231668   -  cellular response to cytokine stimulus\n",
      "\n",
      "Other Gene number: 423\n",
      "############################## Cluster 10 ##############################\n",
      "\n",
      "Cell Num: 84\n",
      "Gene Num: 59\n",
      "Not Zero: 252\n",
      "Cluster 10 Gene number: 67\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "Good           Natural killer cell      8.3722    3.3  \n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 59 Group2: 391\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                 go_name\n",
      " GO:0023024         3              2  0.017699  0.618060   -                     MHC class I protein complex binding\n",
      " GO:0038023         5              9  0.025695  0.618060   -                             signaling receptor activity\n",
      " GO:1990405         3              3  0.032107  0.618060   -                                 protein antigen binding\n",
      " GO:0004715         3              3  0.032107  0.618060   -  non-membrane spanning protein tyrosine kinase activity\n",
      " GO:0032393         2              1  0.046499  0.663507   -                           MHC class I receptor activity\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                go_name\n",
      " GO:0005887        12             43  0.039316  0.908699   -  integral component of plasma membrane\n",
      " GO:0005886        29            143  0.044769  0.908699   -                        plasma membrane\n",
      " GO:0016604         2              3  0.130183  0.908699   -                           nuclear body\n",
      " GO:0043235         3              8  0.164111  0.908699   -                       receptor complex\n",
      " GO:0101003         2              4  0.179221  0.908699   -        ficolin-1-rich granule membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                              go_name\n",
      " GO:0050776        10             25  0.009128  0.553001   -        regulation of immune response\n",
      " GO:0007165        11             31  0.012591  0.553001   -                  signal transduction\n",
      " GO:0007229         4              6  0.030546  0.553001   -  integrin-mediated signaling pathway\n",
      " GO:0030101         3              3  0.032107  0.553001   -       natural killer cell activation\n",
      " GO:0030593         4              7  0.043354  0.553001   -                neutrophil chemotaxis\n",
      "\n",
      "Other Gene number: 391\n",
      "############################## Cluster 11 ##############################\n",
      "\n",
      "Cell Num: 109\n",
      "Gene Num: 95\n",
      "Not Zero: 465\n",
      "Cluster 11 Gene number: 100\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?                    Monocyte           6.7718    1.2  \n",
      "------------------------------------------------------------\n",
      "                  (Macrophage)         (5.5543)\n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 95 Group2: 405\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                              go_name\n",
      " GO:0042802        19             40  0.006977  0.624667   -            identical protein binding\n",
      " GO:0042605         8             10  0.010574  0.624667   -              peptide antigen binding\n",
      " GO:0032395         4              4  0.046174  0.624667   -       MHC class II receptor activity\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " GO:0002020         4              4  0.046174  0.624667   -                     protease binding\n",
      " GO:0046982         7             13  0.064903  0.624667   -  protein heterodimerization activity\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                     go_name\n",
      " GO:0043231        15             17  0.000185  0.031820   *    intracellular membrane-bounded organelle\n",
      " GO:0005765        15             20  0.000635  0.042873   *                          lysosomal membrane\n",
      " GO:0070062        41            104  0.000748  0.042873   *                       extracellular exosome\n",
      " GO:0042613        10             10  0.001364  0.049812   *                MHC class II protein complex\n",
      " GO:0030669         9              8  0.001448  0.049812   *  clathrin-coated endocytic vesicle membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num       p-value   q-value  sig                                                                            go_name\n",
      " GO:0043312        31             42  3.492892e-07  0.000265  ***                                                           neutrophil degranulation\n",
      " GO:0019886        14             16  3.337393e-04  0.126821    -  antigen processing and presentation of exogenous peptide antigen via MHC class II\n",
      " GO:0048013         7              6  4.623113e-03  0.580041    -                                                  ephrin receptor signaling pathway\n",
      " GO:0002576         7              9  1.862982e-02  0.580041    -                                                             platelet degranulation\n",
      " GO:0071222         6              7  2.208856e-02  0.580041    -                                            cellular response to lipopolysaccharide\n",
      "\n",
      "Other Gene number: 405\n",
      "############################## Cluster 12 ##############################\n",
      "\n",
      "Cell Num: 124\n",
      "Gene Num: 81\n",
      "Not Zero: 409\n",
      "Cluster 12 Gene number: 91\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "Good                  B cell            10.5039   6.3  \n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 81 Group2: 380\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                                go_name\n",
      " GO:0023026         6              7  0.014952  0.710186   -                                   MHC class II protein complex binding\n",
      " GO:0042605         7             10  0.017438  0.710186   -                                                peptide antigen binding\n",
      " GO:0044212         4              3  0.020350  0.710186   -                            transcription regulatory region DNA binding\n",
      " GO:0000981        12             27  0.025497  0.710186   -  DNA-binding transcription factor activity, RNA polymerase II-specific\n",
      " GO:0000977         5              6  0.028637  0.710186   -      RNA polymerase II regulatory region sequence-specific DNA binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                     go_name\n",
      " GO:0042613        10             10  0.000681  0.075424   -                MHC class II protein complex\n",
      " GO:0005765        13             19  0.001226  0.075424   -                          lysosomal membrane\n",
      " GO:0030658         8              8  0.002528  0.103663   -                  transport vesicle membrane\n",
      " GO:0030669         8              9  0.004094  0.125890   -  clathrin-coated endocytic vesicle membrane\n",
      " GO:0030666         8             10  0.006318  0.129517   -                  endocytic vesicle membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value  q-value sig                                                                            go_name\n",
      " GO:0050853         7              6  0.002832  0.61201   -                                                  B cell receptor signaling pathway\n",
      " GO:0006959         5              4  0.010485  0.61201   -                                                            humoral immune response\n",
      " GO:0019886        10             17  0.010504  0.61201   -  antigen processing and presentation of exogenous peptide antigen via MHC class II\n",
      " GO:0030154         6              7  0.014952  0.61201   -                                                               cell differentiation\n",
      " GO:0042113         3              1  0.018350  0.61201   -                                                                  B cell activation\n",
      "\n",
      "Other Gene number: 380\n",
      "############################## Cluster 13 ##############################\n",
      "\n",
      "Cell Num: 97\n",
      "Gene Num: 95\n",
      "Not Zero: 410\n",
      "Cluster 13 Gene number: 100\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?          Plasmacytoid dendritic cell  7.3157    1.5  \n",
      "------------------------------------------------------------\n",
      "                    (B cell)           (4.7524)\n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 95 Group2: 385\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                  go_name\n",
      " GO:0019899         7             10  0.033080  0.755226   -                                           enzyme binding\n",
      " GO:0008047         3              2  0.055376  0.755226   -                                enzyme activator activity\n",
      " GO:0042803        12             29  0.086390  0.755226   -                        protein homodimerization activity\n",
      " GO:0016684         2              1  0.101405  0.755226   -  oxidoreductase activity, acting on peroxide as acceptor\n",
      " GO:0031210         2              1  0.101405  0.755226   -                              phosphatidylcholine binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                         go_name\n",
      " GO:0005759         3              1  0.025854  0.697166   -            mitochondrial matrix\n",
      " GO:0005789         9             15  0.030369  0.697166   -  endoplasmic reticulum membrane\n",
      " GO:0005764        11             21  0.033210  0.697166   -                        lysosome\n",
      " GO:0005783        11             21  0.033210  0.697166   -           endoplasmic reticulum\n",
      " GO:0005788         6              9  0.055464  0.697166   -     endoplasmic reticulum lumen\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                      go_name\n",
      " GO:0043312        21             47  0.012772  0.629339   -                                     neutrophil degranulation\n",
      " GO:0033138         3              1  0.025854  0.629339   -       positive regulation of peptidyl-serine phosphorylation\n",
      " GO:1903206         3              1  0.025854  0.629339   -  negative regulation of hydrogen peroxide-induced cell death\n",
      " GO:0008203         3              1  0.025854  0.629339   -                                cholesterol metabolic process\n",
      " GO:0010629         6              7  0.026793  0.629339   -                       negative regulation of gene expression\n",
      "\n",
      "Other Gene number: 385\n",
      "############################## Cluster 2 ##############################\n",
      "\n",
      "Cell Num: 140\n",
      "Gene Num: 44\n",
      "Not Zero: 322\n",
      "Cluster 2 Gene number: 47\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?              Natural killer cell      6.9186    1.4  \n",
      "------------------------------------------------------------\n",
      "                    (T cell)           (5.0021)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 44 Group2: 413\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value  q-value sig                                go_name\n",
      " GO:0005102         7             22  0.014526  0.49506   -             signaling receptor binding\n",
      " GO:0004725         2              2  0.047997  0.49506   -  protein tyrosine phosphatase activity\n",
      " GO:0031726         2              3  0.075138  0.49506   -        CCR1 chemokine receptor binding\n",
      " GO:0031730         2              4  0.105911  0.49506   -        CCR5 chemokine receptor binding\n",
      " GO:0042288         2              4  0.105911  0.49506   -            MHC class I protein binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                      go_name\n",
      " GO:0042612         3              3  0.013590  0.709586   -  MHC class I protein complex\n",
      " GO:0031901         4             10  0.036610  0.709586   -      early endosome membrane\n",
      " GO:0055038         3              6  0.046382  0.709586   -  recycling endosome membrane\n",
      " GO:0030670         3              7  0.061864  0.709586   -  phagocytic vesicle membrane\n",
      " GO:0005576        14             84  0.062224  0.709586   -         extracellular region\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                                                            go_name\n",
      " GO:0050776        11             27  0.000331  0.118059   -                                                                      regulation of immune response\n",
      " GO:0002474         3              3  0.013590  0.401857   -                             antigen processing and presentation of peptide antigen via MHC class I\n",
      " GO:0002480         3              3  0.013590  0.401857   -  antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent\n",
      " GO:0007267         4              7  0.014991  0.401857   -                                                                                cell-cell signaling\n",
      " GO:0001916         4              8  0.020916  0.401857   -                                                positive regulation of T cell mediated cytotoxicity\n",
      "\n",
      "Other Gene number: 413\n",
      "############################## Cluster 3 ##############################\n",
      "\n",
      "Cell Num: 61\n",
      "Gene Num: 29\n",
      "Not Zero: 144\n",
      "Cluster 3 Gene number: 31\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?              Natural killer cell      5.1319    1.5  \n",
      "------------------------------------------------------------\n",
      "          (Natural killer T (NKT) cell)(3.4568)\n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 29 Group2: 423\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                              go_name\n",
      " GO:0042288         3              4  0.007006  0.366452   -          MHC class I protein binding\n",
      " GO:0008009         3              7  0.021045  0.366452   -                   chemokine activity\n",
      " GO:0042379         2              2  0.022029  0.366452   -           chemokine receptor binding\n",
      " GO:0015026         3              8  0.027693  0.366452   -                  coreceptor activity\n",
      " GO:0023024         2              3  0.035257  0.366452   -  MHC class I protein complex binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                           go_name\n",
      " GO:0044194         2              2  0.022029  0.482012   -                 cytolytic granule\n",
      " GO:0005886        16            158  0.045106  0.482012   -                   plasma membrane\n",
      " GO:0042101         2              4  0.050794  0.482012   -           T cell receptor complex\n",
      " GO:0009897         6             38  0.051134  0.482012   -  external side of plasma membrane\n",
      " GO:0099524         1              1  0.124335  0.482012   -              postsynaptic cytosol\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                                    go_name\n",
      " GO:0045954         3              5  0.010726  0.353809   -           positive regulation of natural killer cell mediated cytotoxicity\n",
      " GO:0042059         2              1  0.011472  0.353809   -  negative regulation of epidermal growth factor receptor signaling pathway\n",
      " GO:0042110         3              6  0.015395  0.353809   -                                                          T cell activation\n",
      " GO:0070098         3              6  0.015395  0.353809   -                                       chemokine-mediated signaling pathway\n",
      " GO:0007169         3              7  0.021045  0.353809   -           transmembrane receptor protein tyrosine kinase signaling pathway\n",
      "\n",
      "Other Gene number: 423\n",
      "############################## Cluster 4 ##############################\n",
      "\n",
      "Cell Num: 24\n",
      "Gene Num: 13\n",
      "Not Zero: 42\n",
      "Cluster 4 Gene number: 17\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?              Natural killer cell      3.4818    1.4  \n",
      "------------------------------------------------------------\n",
      "                (Microglial cell)      (2.5759)\n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 13 Group2: 429\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                          go_name\n",
      " GO:0008009         4              6  0.000087  0.002599  **               chemokine activity\n",
      " GO:0031726         3              2  0.000193  0.002899  **  CCR1 chemokine receptor binding\n",
      " GO:0031730         3              3  0.000380  0.003800  **  CCR5 chemokine receptor binding\n",
      " GO:0048020         3              4  0.000654  0.004902  **   CCR chemokine receptor binding\n",
      " GO:0042056         2              1  0.002361  0.011805   *         chemoattractant activity\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                go_name\n",
      " GO:0005576         6             85  0.032121  0.449691   -                   extracellular region\n",
      " GO:0005575         1              3  0.112925  0.627115   -                     cellular_component\n",
      " GO:0005615         4             66  0.134382  0.627115   -                    extracellular space\n",
      " GO:0005788         1             12  0.325336  0.989981   -            endoplasmic reticulum lumen\n",
      " GO:0005887         2             50  0.465103  0.989981   -  integral component of plasma membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                go_name\n",
      " GO:0048245         3              2  0.000193  0.010551   *                                  eosinophil chemotaxis\n",
      " GO:0043922         3              2  0.000193  0.010551   *     negative regulation by host of viral transcription\n",
      " GO:2000503         3              3  0.000380  0.010551   *  positive regulation of natural killer cell chemotaxis\n",
      " GO:0009636         3              3  0.000380  0.010551   *                            response to toxic substance\n",
      " GO:0051928         3              4  0.000654  0.010551   *           positive regulation of calcium ion transport\n",
      "\n",
      "Other Gene number: 429\n",
      "############################## Cluster 5 ##############################\n",
      "\n",
      "Cell Num: 113\n",
      "Gene Num: 62\n",
      "Not Zero: 293\n",
      "Cluster 5 Gene number: 66\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Good       Natural killer T (NKT) cell  6.9832    2.0  \n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 62 Group2: 409\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num       p-value   q-value  sig                                 go_name\n",
      " GO:0003723        22             33  6.178618e-08  0.000009  ***                             RNA binding\n",
      " GO:0003743         4              1  1.240823e-03  0.090580    -  translation initiation factor activity\n",
      " GO:0045296         8             12  2.018774e-03  0.097927    -                        cadherin binding\n",
      " GO:0003746         4              2  3.353669e-03  0.097927    -  translation elongation factor activity\n",
      " GO:0003785         4              2  3.353669e-03  0.097927    -                   actin monomer binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                    go_name\n",
      " GO:0005634        37            125  0.000011  0.001776  **                    nucleus\n",
      " GO:1990904         8              6  0.000093  0.007532  **  ribonucleoprotein complex\n",
      " GO:0005829        32            117  0.000356  0.019199   *                    cytosol\n",
      " GO:0016020        22             77  0.003378  0.132198   -                   membrane\n",
      " GO:0070062        27            106  0.004080  0.132198   -      extracellular exosome\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                 go_name\n",
      " GO:0006413         6              3  0.000254  0.115402   -                translational initiation\n",
      " GO:0006446         4              1  0.001241  0.282287   -  regulation of translational initiation\n",
      " GO:0043488         4              2  0.003354  0.381480   -            regulation of mRNA stability\n",
      " GO:0006414         4              2  0.003354  0.381480   -                translational elongation\n",
      " GO:0045727         5              5  0.005047  0.459248   -      positive regulation of translation\n",
      "\n",
      "Other Gene number: 409\n",
      "############################## Cluster 6 ##############################\n",
      "\n",
      "Cell Num: 73\n",
      "Gene Num: 15\n",
      "Not Zero: 103\n",
      "Cluster 6 Gene number: 16\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?             Mesenchymal stem cell     4.7201    1.4  \n",
      "------------------------------------------------------------\n",
      "          (Natural killer T (NKT) cell)(3.3797)\n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 15 Group2: 426\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                      go_name\n",
      " GO:0008270         2              9  0.049777  0.411961   -             zinc ion binding\n",
      " GO:0008266         1              1  0.066945  0.411961   -          poly(U) RNA binding\n",
      " GO:0004126         1              1  0.066945  0.411961   -  cytidine deaminase activity\n",
      " GO:0000049         1              2  0.098826  0.411961   -                 tRNA binding\n",
      " GO:0019960         1              2  0.098826  0.411961   -     C-X3-C chemokine binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                      go_name\n",
      " GO:0042612         2              3  0.010195  0.230716   -  MHC class I protein complex\n",
      " GO:0055038         2              6  0.026893  0.230716   -  recycling endosome membrane\n",
      " GO:0030670         2              7  0.033898  0.230716   -  phagocytic vesicle membrane\n",
      " GO:0032587         2             10  0.058563  0.230716   -              ruffle membrane\n",
      " GO:0031901         2             10  0.058563  0.230716   -      early endosome membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                                                            go_name\n",
      " GO:0002474         2              3  0.010195  0.186822   -                             antigen processing and presentation of peptide antigen via MHC class I\n",
      " GO:0002480         2              3  0.010195  0.186822   -  antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent\n",
      " GO:0002479         2              4  0.014991  0.186822   -    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent\n",
      " GO:0006909         2              5  0.020574  0.186822   -                                                                                       phagocytosis\n",
      " GO:0050776         4             30  0.021924  0.186822   -                                                                      regulation of immune response\n",
      "\n",
      "Other Gene number: 426\n",
      "############################## Cluster 7 ##############################\n",
      "\n",
      "Cell Num: 38\n",
      "Gene Num: 17\n",
      "Not Zero: 69\n",
      "Cluster 7 Gene number: 20\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?              Natural killer cell      3.6352    1.3  \n",
      "------------------------------------------------------------\n",
      "             (T helper1 (Th1) cell)    (2.8579)\n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 17 Group2: 422\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value  q-value sig                                       go_name\n",
      " GO:0005125         2              6  0.034487  0.26655   -                             cytokine activity\n",
      " GO:0044877         2              6  0.034487  0.26655   -            protein-containing complex binding\n",
      " GO:0004867         2              6  0.034487  0.26655   -  serine-type endopeptidase inhibitor activity\n",
      " GO:0051920         1              1  0.076034  0.26655   -                        peroxiredoxin activity\n",
      " GO:0019958         1              1  0.076034  0.26655   -                       C-X-C chemokine binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                  go_name\n",
      " GO:0005623         2              1  0.004147  0.153426   -                                                     cell\n",
      " GO:0000786         1              1  0.076034  0.387450   -                                               nucleosome\n",
      " GO:0045092         1              1  0.076034  0.387450   -                          interleukin-18 receptor complex\n",
      " GO:0035861         1              1  0.076034  0.387450   -                              site of double-strand break\n",
      " GO:0031232         1              1  0.076034  0.387450   -  extrinsic component of external side of plasma membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                   go_name\n",
      " GO:0045429         2              3  0.013198  0.184325   -  positive regulation of nitric oxide biosynthetic process\n",
      " GO:0006281         2              3  0.013198  0.184325   -                                                DNA repair\n",
      " GO:0010469         3             14  0.023465  0.184325   -                 regulation of signaling receptor activity\n",
      " GO:0009615         3             14  0.023465  0.184325   -                                         response to virus\n",
      " GO:0007283         2              5  0.026467  0.184325   -                                           spermatogenesis\n",
      "\n",
      "Other Gene number: 422\n",
      "############################## Cluster 8 ##############################\n",
      "\n",
      "Cell Num: 81\n",
      "Gene Num: 96\n",
      "Not Zero: 423\n",
      "Cluster 8 Gene number: 100\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Good                  B cell            7.6341    2.1  \n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 96 Group2: 414\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                 go_name\n",
      " GO:0042605         8             10  0.009994  0.673938   -                 peptide antigen binding\n",
      " GO:0032395         4              4  0.044773  0.673938   -          MHC class II receptor activity\n",
      " GO:0019864         3              2  0.048423  0.673938   -                             IgG binding\n",
      " GO:0005200         5              7  0.055748  0.673938   -  structural constituent of cytoskeleton\n",
      " GO:0023026         5              8  0.077375  0.673938   -    MHC class II protein complex binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                       go_name\n",
      " GO:0042613        10             10  0.001267  0.130663   -  MHC class II protein complex\n",
      " GO:0032588        10             11  0.002040  0.130663   -  trans-Golgi network membrane\n",
      " GO:0005765        14             22  0.002839  0.130663   -            lysosomal membrane\n",
      " GO:0030666         9             10  0.003662  0.130663   -    endocytic vesicle membrane\n",
      " GO:0030658         8              8  0.004113  0.130663   -    transport vesicle membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                                                            go_name\n",
      " GO:0019886        14             16  0.000302  0.240396   -  antigen processing and presentation of exogenous peptide antigen via MHC class II\n",
      " GO:0043312        23             50  0.003399  0.611087   -                                                           neutrophil degranulation\n",
      " GO:0050766         4              3  0.026119  0.611087   -                                                positive regulation of phagocytosis\n",
      " GO:0006911         4              3  0.026119  0.611087   -                                                           phagocytosis, engulfment\n",
      " GO:0050852         7             11  0.035450  0.611087   -                                                  T cell receptor signaling pathway\n",
      "\n",
      "Other Gene number: 414\n",
      "############################## Cluster 9 ##############################\n",
      "\n",
      "Cell Num: 150\n",
      "Gene Num: 43\n",
      "Not Zero: 333\n",
      "Cluster 9 Gene number: 46\n",
      "------------------------------------------------------------\n",
      "Type                Cell Type           Score     Times\n",
      "------------------------------------------------------------\n",
      "?                     T cell            5.9454    1.2  \n",
      "------------------------------------------------------------\n",
      "          (Natural killer T (NKT) cell)(5.0754)\n",
      "------------------------------------------------------------\n",
      "\n",
      "Go Enrichment analysis: Group1: 43 Group2: 415\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Function <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                            go_name\n",
      " GO:0005509         6             16  0.011431  0.458425   -                calcium ion binding\n",
      " GO:0042393         3              3  0.012653  0.458425   -                    histone binding\n",
      " GO:0004860         2              1  0.024334  0.458425   -  protein kinase inhibitor activity\n",
      " GO:0048306         3              5  0.030958  0.458425   -  calcium-dependent protein binding\n",
      " GO:0019901         5             16  0.037568  0.458425   -             protein kinase binding\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Component <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                         go_name\n",
      " GO:0031966         3              2  0.006770  0.531758   -          mitochondrial membrane\n",
      " GO:0005575         3              3  0.012653  0.531758   -              cellular_component\n",
      " GO:0032991         6             21  0.031514  0.531758   -      protein-containing complex\n",
      " GO:0005730         4             10  0.033662  0.531758   -                       nucleolus\n",
      " GO:0031225         2              2  0.045769  0.531758   -  anchored component of membrane\n",
      "\n",
      ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Process <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n",
      "        ids  gene_num  othergene_num   p-value   q-value sig                                          go_name\n",
      " GO:0051607         9             11  0.000019  0.003792  **                        defense response to virus\n",
      " GO:0060337         7              5  0.000022  0.003792  **              type I interferon signaling pathway\n",
      " GO:0045071         4              3  0.001929  0.219856   -  negative regulation of viral genome replication\n",
      " GO:0034113         3              2  0.006770  0.380543   -                   heterotypic cell-cell adhesion\n",
      " GO:0035455         2              1  0.024334  0.380543   -                     response to interferon-alpha\n",
      "\n",
      "Other Gene number: 415\n",
      "################################################################################\n",
      "\n",
      "#Cluster Type Celltype Score Times\n",
      "['0', 'N', '-', '-', '-']\n",
      "['1', '?', 'Naive T cell|Central memory T cell', '4.520441841545353|3.0610204857441494', 1.476776082550918]\n",
      "['10', 'Good', 'Natural killer cell', 8.372211745146492, 3.27145242050666]\n",
      "['11', '?', 'Monocyte|Macrophage', '6.771772654422211|5.554336470517134', 1.2191866103840354]\n",
      "['12', 'Good', 'B cell', 10.503924714174651, 6.343198632076636]\n",
      "['13', '?', 'Plasmacytoid dendritic cell|B cell', '7.315730734273448|4.752392406029024', 1.5393785085996892]\n",
      "['2', '?', 'Natural killer cell|T cell', '6.918572227095394|5.002145910384388', 1.3831208347466497]\n",
      "['3', '?', 'Natural killer cell|Natural killer T (NKT) cell', '5.131942264998032|3.4567651246965525', 1.4846083201700122]\n",
      "['4', '?', 'Natural killer cell|Microglial cell', '3.481761556652867|2.575868037432298', 1.3516847548306825]\n",
      "['5', 'Good', 'Natural killer T (NKT) cell', 6.983178426005285, 2.0383405119549494]\n",
      "['6', '?', 'Mesenchymal stem cell|Natural killer T (NKT) cell', '4.7201012826677005|3.379735383167512', 1.3965890069902418]\n",
      "['7', '?', 'Natural killer cell|T helper1 (Th1) cell', '3.6351589676122873|2.8578858045304383', 1.271974885018038]\n",
      "['8', 'Good', 'B cell', 7.634067181630303, 2.147147479432095]\n",
      "['9', '?', 'T cell|Natural killer T (NKT) cell', '5.945447997544145|5.07542770594091', 1.1714181231632668]\n"
     ]
    }
   ],
   "source": [
    "python3 SCSA.py -d whole.db -i /scratch/umap_cluster.csv -s scanpy -E -f1.5 -p 0.01 -o /scratch/umap_annotation_result -m txt "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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   "file_extension": ".sh",
   "mimetype": "text/x-sh",
   "name": "bash"
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