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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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TF_cistrome_correlation #341

Open hanapac opened 6 months ago

hanapac commented 6 months ago

Thank you for creating scenicplus, I got far in the analysis. I am trying to calculate my TF_cistrome_correlation using:

from scenicplus.cistromes import TF_cistrome_correlation, generate_pseudobulks

generate_pseudobulks(
        scplus_obj = scplus_obj,
        variable = 'GEX_cell_type',
        auc_key = 'eRegulon_AUC_filtered',
        signature_key = 'Gene_based')
generate_pseudobulks(
        scplus_obj = scplus_obj,
        variable = 'GEX_cell_type',
        auc_key = 'eRegulon_AUC_filtered',
        signature_key = 'Region_based')

TF_cistrome_correlation(
            scplus_obj,
            use_pseudobulk = True,
            variable = 'GEX_cell_type',
            auc_key = 'eRegulon_AUC_filtered',
            signature_key = 'Gene_based',
            out_key = 'filtered_gene_based')
TF_cistrome_correlation(
            scplus_obj,
            use_pseudobulk = True,
            variable = 'GEX_cell_type',
            auc_key = 'eRegulon_AUC_filtered',
            signature_key = 'Region_based',
            out_key = 'filtered_region_based')

The code runs withut errors, however, the result is an empty dataframe: scplus_obj.uns['TF_cistrome_correlation']['filtered_gene_based'].shape (0, 5)

How can I solve this? I was able to reproduce the PBMC tutorial including this part. Thank you in advance.

scenicplus.version '1.0.1.dev4+ge4bdd9f'

SeppeDeWinter commented 6 months ago

Hi @hanapac

Thank you for the nice comments.

Can you show


scplus_obj.uns["Pseudobulk"]

All the best,

Seppe

hanapac commented 6 months ago 
scplus_obj.uns["Pseudobulk"]
​
{'GEX_cell_type': {'Expression':              Pro B_0  Pro B_1  Pro B_2  Pro B_3  Pro B_4  Pro B_5  Pro B_6  \
  MIR1302-2HG      0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  AL627309.1       0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  AL627309.3       0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  AL627309.5       0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  AL627309.4       0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  ...              ...      ...      ...      ...      ...      ...      ...   
  AC141272.1       0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  AC023491.2       0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  AC007325.1       0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  AC007325.4       0.0      0.0      0.0      0.0      0.0      0.0      0.0   
  AC007325.2       0.0      0.0      0.0      0.0      0.0      0.0      0.0   

               Pro B_7  Pro B_8  Pro B_9  ...  Immature B_90  Immature B_91  \
  MIR1302-2HG      0.0      0.0      0.0  ...        0.00000            0.0   
  AL627309.1       0.0      0.0      0.0  ...        0.00000            0.0   
  AL627309.3       0.0      0.0      0.0  ...        0.00000            0.0   
  AL627309.5       0.0      0.0      0.0  ...        0.62472            0.0   
  AL627309.4       0.0      0.0      0.0  ...        0.00000            0.0   
  ...              ...      ...      ...  ...            ...            ...   
  AC141272.1       0.0      0.0      0.0  ...        0.00000            0.0   
  AC023491.2       0.0      0.0      0.0  ...        0.00000            0.0   
  AC007325.1       0.0      0.0      0.0  ...        0.00000            0.0   
  AC007325.4       0.0      0.0      0.0  ...        0.00000            0.0   
  AC007325.2       0.0      0.0      0.0  ...        0.00000            0.0   

               Immature B_92  Immature B_93  Immature B_94  Immature B_95  \
  MIR1302-2HG            0.0            0.0            0.0       0.000000   
  AL627309.1             0.0            0.0            0.0       0.000000   
  AL627309.3             0.0            0.0            0.0       0.000000   
  AL627309.5             0.0            0.0            0.0       0.000000   
  AL627309.4             0.0            0.0            0.0       0.000000   
  ...                    ...            ...            ...            ...   
  AC141272.1             0.0            0.0            0.0       0.000000   
  AC023491.2             0.0            0.0            0.0       0.733038   
  AC007325.1             0.0            0.0            0.0       0.000000   
  AC007325.4             0.0            0.0            0.0       0.000000   
  AC007325.2             0.0            0.0            0.0       0.000000   

               Immature B_96  Immature B_97  Immature B_98  Immature B_99  
  MIR1302-2HG            0.0            0.0            0.0            0.0  
  AL627309.1             0.0            0.0            0.0            0.0  
  AL627309.3             0.0            0.0            0.0            0.0  
  AL627309.5             0.0            0.0            0.0            0.0  
  AL627309.4             0.0            0.0            0.0            0.0  
  ...                    ...            ...            ...            ...  
  AC141272.1             0.0            0.0            0.0            0.0  
  AC023491.2             0.0            0.0            0.0            0.0  
  AC007325.1             0.0            0.0            0.0            0.0  
  AC007325.4             0.0            0.0            0.0            0.0  
  AC007325.2             0.0            0.0            0.0            0.0  

  [33685 rows x 500 columns],
  'eRegulon_AUC': {'Gene_based':                            Pro B_0   Pro B_1   Pro B_2   Pro B_3   Pro B_4  \
   MAFB_extended_+_-_(13g)   0.019496  0.011630  0.039393  0.025562  0.028540   
   ZNF223_+_-_(24g)          0.024688  0.029399  0.031943  0.035506  0.023179   
   VDR_extended_+_+_(44g)    0.121337  0.108165  0.106842  0.112003  0.071224   
   MEF2C_extended_+_+_(16g)  0.192488  0.247974  0.231079  0.241427  0.296548   
   ZNF2_extended_+_-_(25g)   0.028556  0.015914  0.025615  0.024812  0.005102   
   ...                            ...       ...       ...       ...       ...   
   JUNB_extended_+_-_(85g)   0.225717  0.283349  0.371896  0.205416  0.186065   
   THRB_extended_+_+_(64g)   0.060965  0.064380  0.066178  0.061012  0.047051   
   CREB3_extended_+_+_(43g)  0.020502  0.022281  0.021618  0.015183  0.020267   
   ZNF501_+_+_(42g)          0.030342  0.023640  0.037292  0.043601  0.037595   
   RARA_+_-_(11g)            0.130652  0.062978  0.123958  0.080404  0.064975   

                              Pro B_5   Pro B_6   Pro B_7   Pro B_8   Pro B_9  \
   MAFB_extended_+_-_(13g)   0.033757  0.038653  0.011995  0.006441  0.065960   
   ZNF223_+_-_(24g)          0.029439  0.017993  0.025520  0.048035  0.015058   
   VDR_extended_+_+_(44g)    0.104284  0.115259  0.104008  0.112352  0.133478   
   MEF2C_extended_+_+_(16g)  0.241590  0.252249  0.280545  0.187159  0.254305   
   ZNF2_extended_+_-_(25g)   0.017169  0.020931  0.001995  0.022489  0.017145   
   ...                            ...       ...       ...       ...       ...   
   JUNB_extended_+_-_(85g)   0.351061  0.406233  0.182458  0.188610  0.243581   
   THRB_extended_+_+_(64g)   0.063818  0.056851  0.063587  0.070192  0.061004   
   CREB3_extended_+_+_(43g)  0.014056  0.045294  0.026087  0.021822  0.021115   
   ZNF501_+_+_(42g)          0.011865  0.031798  0.036175  0.045083  0.030930   
   RARA_+_-_(11g)            0.039106  0.074779  0.127607  0.054707  0.049957   

                             ...  Pre Bl_90  Pre Bl_91  Pre Bl_92  Pre Bl_93  \
   MAFB_extended_+_-_(13g)   ...   0.014078   0.035017   0.113822   0.051517   
   ZNF223_+_-_(24g)          ...   0.027727   0.018131   0.013737   0.015499   
   VDR_extended_+_+_(44g)    ...   0.082493   0.115855   0.097528   0.094534   
   MEF2C_extended_+_+_(16g)  ...   0.216924   0.254572   0.214638   0.259412   
   ZNF2_extended_+_-_(25g)   ...   0.035121   0.026185   0.049387   0.003525   
   ...                       ...        ...        ...        ...        ...   
   JUNB_extended_+_-_(85g)   ...   0.353796   0.311130   0.268815   0.220232   
   THRB_extended_+_+_(64g)   ...   0.040872   0.042958   0.039148   0.036581   
   CREB3_extended_+_+_(43g)  ...   0.019284   0.016279   0.021563   0.018754   
   ZNF501_+_+_(42g)          ...   0.029205   0.031179   0.019828   0.025648   
   RARA_+_-_(11g)            ...   0.049946   0.087843   0.084107   0.067340   

                             Pre Bl_94  Pre Bl_95  Pre Bl_96  Pre Bl_97  \
   MAFB_extended_+_-_(13g)    0.026302   0.079280   0.018290   0.065823   
   ZNF223_+_-_(24g)           0.029092   0.028424   0.019928   0.035882   
   VDR_extended_+_+_(44g)     0.065067   0.077966   0.086652   0.089613   
   MEF2C_extended_+_+_(16g)   0.238279   0.227999   0.189808   0.258306   
   ZNF2_extended_+_-_(25g)    0.011748   0.019620   0.022019   0.020048   
   ...                             ...        ...        ...        ...   
   JUNB_extended_+_-_(85g)    0.259962   0.321128   0.369982   0.296037   
   THRB_extended_+_+_(64g)    0.028299   0.040740   0.040978   0.040731   
   CREB3_extended_+_+_(43g)   0.019500   0.020022   0.030484   0.034367   
   ZNF501_+_+_(42g)           0.041559   0.017402   0.020583   0.027169   
   RARA_+_-_(11g)             0.087292   0.079216   0.082315   0.085813   

                             Pre Bl_98  Pre Bl_99  
   MAFB_extended_+_-_(13g)    0.065595   0.038599  
   ZNF223_+_-_(24g)           0.031280   0.019047  
   VDR_extended_+_+_(44g)     0.069750   0.101857  
   MEF2C_extended_+_+_(16g)   0.156302   0.189519  
   ZNF2_extended_+_-_(25g)    0.015264   0.026499  
   ...                             ...        ...  
   JUNB_extended_+_-_(85g)    0.265634   0.333854  
   THRB_extended_+_+_(64g)    0.038248   0.046201  
   CREB3_extended_+_+_(43g)   0.016635   0.021148  
   ZNF501_+_+_(42g)           0.023804   0.035420  
   RARA_+_-_(11g)             0.062233   0.097193  

   [992 rows x 500 columns],
   'Region_based':                             Pro B_0   Pro B_1   Pro B_2   Pro B_3   Pro B_4  \
   E4F1_extended_+_-_(45r)    0.765231  0.768987  0.771442  0.756633  0.760976   
   BATF3_+_+_(28r)            0.060814  0.030485  0.028447  0.043895  0.029135   
   CEBPD_+_-_(28r)            0.279304  0.255242  0.263495  0.259202  0.231223   
   ZNF48_extended_+_-_(20r)   0.134624  0.150916  0.130145  0.115564  0.123863   
   DRAP1_extended_+_+_(63r)   0.836709  0.840811  0.839327  0.833154  0.833744   
   ...                             ...       ...       ...       ...       ...   
   SP2_+_+_(238r)             0.154110  0.153896  0.151854  0.154792  0.153050   
   THAP1_+_-_(33r)            0.510776  0.512157  0.510455  0.506287  0.509451   
   CREB1_extended_+_+_(45r)   0.310989  0.308042  0.316189  0.312913  0.318113   
   IKZF1_extended_+_+_(648r)  0.020646  0.014990  0.022643  0.022490  0.020000   
   MBD2_extended_-_+_(20r)    0.782369  0.789446  0.786486  0.773777  0.777813   

                               Pro B_5   Pro B_6   Pro B_7   Pro B_8   Pro B_9  \
   E4F1_extended_+_-_(45r)    0.770542  0.769078  0.768109  0.764245  0.768229   
   BATF3_+_+_(28r)            0.023107  0.030544  0.051204  0.050557  0.036671   
   CEBPD_+_-_(28r)            0.249032  0.245149  0.257387  0.274359  0.256404   
   ZNF48_extended_+_-_(20r)   0.145581  0.133800  0.145045  0.133103  0.141450   
   DRAP1_extended_+_+_(63r)   0.842073  0.840730  0.839479  0.838199  0.841051   
   ...                             ...       ...       ...       ...       ...   
   SP2_+_+_(238r)             0.150764  0.154048  0.157863  0.158672  0.153623   
   THAP1_+_-_(33r)            0.515015  0.512899  0.509519  0.506071  0.511183   
   CREB1_extended_+_+_(45r)   0.308679  0.314972  0.307049  0.309526  0.310693   
   IKZF1_extended_+_+_(648r)  0.015370  0.016992  0.017521  0.020800  0.018255   
   MBD2_extended_-_+_(20r)    0.792826  0.788589  0.781803  0.783671  0.789671   

                              ...  Pre Bl_90  Pre Bl_91  Pre Bl_92  Pre Bl_93  \
   E4F1_extended_+_-_(45r)    ...   0.765778   0.751184   0.759888   0.762970   
   BATF3_+_+_(28r)            ...   0.019166   0.047217   0.019538   0.018101   
   CEBPD_+_-_(28r)            ...   0.208826   0.213218   0.214871   0.204206   
   ZNF48_extended_+_-_(20r)   ...   0.129364   0.116062   0.122121   0.123093   
   DRAP1_extended_+_+_(63r)   ...   0.835180   0.824343   0.828676   0.832912   
   ...                        ...        ...        ...        ...        ...   
   SP2_+_+_(238r)             ...   0.148299   0.153272   0.147014   0.147042   
   THAP1_+_-_(33r)            ...   0.509847   0.501492   0.508110   0.509159   
   CREB1_extended_+_+_(45r)   ...   0.315599   0.314571   0.313134   0.310012   
   IKZF1_extended_+_+_(648r)  ...   0.018415   0.023133   0.021065   0.023295   
   MBD2_extended_-_+_(20r)    ...   0.779681   0.760818   0.773378   0.777519   

                              Pre Bl_94  Pre Bl_95  Pre Bl_96  Pre Bl_97  \
   E4F1_extended_+_-_(45r)     0.772344   0.765369   0.767441   0.767745   
   BATF3_+_+_(28r)             0.021720   0.041625   0.018909   0.022757   
   CEBPD_+_-_(28r)             0.248799   0.258922   0.211292   0.231976   
   ZNF48_extended_+_-_(20r)    0.128180   0.131178   0.120427   0.129831   
   DRAP1_extended_+_+_(63r)    0.838485   0.833353   0.834161   0.836279   
   ...                              ...        ...        ...        ...   
   SP2_+_+_(238r)              0.147220   0.150407   0.147256   0.147528   
   THAP1_+_-_(33r)             0.512256   0.508418   0.509060   0.509541   
   CREB1_extended_+_+_(45r)    0.313512   0.321533   0.325695   0.324031   
   IKZF1_extended_+_+_(648r)   0.023597   0.024831   0.021267   0.021369   
   MBD2_extended_-_+_(20r)     0.786999   0.784716   0.780998   0.784847   

                              Pre Bl_98  Pre Bl_99  
   E4F1_extended_+_-_(45r)     0.765905   0.774709  
   BATF3_+_+_(28r)             0.018275   0.022439  
   CEBPD_+_-_(28r)             0.212705   0.233743  
   ZNF48_extended_+_-_(20r)    0.128652   0.141415  
   DRAP1_extended_+_+_(63r)    0.835749   0.841627  
   ...                              ...        ...  
   SP2_+_+_(238r)              0.146945   0.149339  
   THAP1_+_-_(33r)             0.513105   0.512587  
   CREB1_extended_+_+_(45r)    0.311641   0.322812  
   IKZF1_extended_+_+_(648r)   0.018330   0.019800  
   MBD2_extended_-_+_(20r)     0.783146   0.792230  

   [992 rows x 500 columns]},
  'eRegulon_AUC_filtered': {'Gene_based':                  Pro B_0   Pro B_1   Pro B_2   Pro B_3   Pro B_4   Pro B_5  \
   ARNTL2_+_(16g)  0.025293  0.031959  0.036609  0.038628  0.036806  0.031996   
   ASCL2_+_(20g)   0.047758  0.050941  0.046615  0.052135  0.043058  0.061143   
   ATF1_+_(11g)    0.058033  0.065839  0.060349  0.070444  0.049601  0.072711   
   ATF5_+_(40g)    0.055917  0.047594  0.050640  0.043751  0.064771  0.063284   
   BACH2_-_(355g)  0.151115  0.161499  0.142408  0.170751  0.140557  0.167725   
   ...                  ...       ...       ...       ...       ...       ...   
   ZNF749_+_(32g)  0.015770  0.054649  0.035737  0.053548  0.029936  0.029420   
   ZNF764_+_(94g)  0.041915  0.045269  0.045758  0.041636  0.045939  0.044645   
   ZNF787_+_(12g)  0.059392  0.061367  0.049010  0.032542  0.062332  0.048842   
   ZNF823_+_(10g)  0.029982  0.027120  0.016033  0.045232  0.019501  0.019798   
   ZNF846_+_(23g)  0.065736  0.072181  0.069710  0.068757  0.085224  0.053372   

                    Pro B_6   Pro B_7   Pro B_8   Pro B_9  ...  Immature B_90  \
   ARNTL2_+_(16g)  0.028318  0.037225  0.017410  0.020851  ...       0.017102   
   ASCL2_+_(20g)   0.042102  0.043248  0.065062  0.050232  ...       0.030098   
   ATF1_+_(11g)    0.087989  0.096502  0.107077  0.093851  ...       0.068533   
   ATF5_+_(40g)    0.042953  0.069014  0.045990  0.057412  ...       0.105490   
   BACH2_-_(355g)  0.174552  0.144296  0.175717  0.169332  ...       0.127530   
   ...                  ...       ...       ...       ...  ...            ...   
   ZNF749_+_(32g)  0.053023  0.025791  0.044706  0.037088  ...       0.040168   
   ZNF764_+_(94g)  0.045193  0.050752  0.045275  0.044307  ...       0.024857   
   ZNF787_+_(12g)  0.070947  0.048159  0.049406  0.067216  ...       0.054815   
   ZNF823_+_(10g)  0.038403  0.024982  0.033593  0.030897  ...       0.027827   
   ZNF846_+_(23g)  0.073704  0.076221  0.081016  0.075374  ...       0.047348   

                   Immature B_91  Immature B_92  Immature B_93  Immature B_94  \
   ARNTL2_+_(16g)       0.020034       0.021148       0.019581       0.027516   
   ASCL2_+_(20g)        0.050062       0.035240       0.022132       0.032850   
   ATF1_+_(11g)         0.120131       0.057941       0.122382       0.066541   
   ATF5_+_(40g)         0.047138       0.037429       0.036945       0.047447   
   BACH2_-_(355g)       0.122916       0.148551       0.122523       0.103631   
   ...                       ...            ...            ...            ...   
   ZNF749_+_(32g)       0.027938       0.035362       0.036105       0.027600   
   ZNF764_+_(94g)       0.030765       0.033526       0.023402       0.023069   
   ZNF787_+_(12g)       0.042686       0.041682       0.041632       0.033195   
   ZNF823_+_(10g)       0.004697       0.014667       0.007910       0.004293   
   ZNF846_+_(23g)       0.074925       0.056664       0.043822       0.045722   

                   Immature B_95  Immature B_96  Immature B_97  Immature B_98  \
   ARNTL2_+_(16g)       0.030274       0.018735       0.025226       0.020899   
   ASCL2_+_(20g)        0.025888       0.014014       0.022963       0.035778   
   ATF1_+_(11g)         0.074260       0.079416       0.081559       0.078217   
   ATF5_+_(40g)         0.042227       0.049227       0.054758       0.042545   
   BACH2_-_(355g)       0.097889       0.099140       0.122861       0.137558   
   ...                       ...            ...            ...            ...   
   ZNF749_+_(32g)       0.026006       0.038270       0.035008       0.030812   
   ZNF764_+_(94g)       0.017055       0.021369       0.026910       0.025015   
   ZNF787_+_(12g)       0.021358       0.045136       0.031621       0.055824   
   ZNF823_+_(10g)       0.008076       0.011033       0.013391       0.014044   
   ZNF846_+_(23g)       0.042882       0.032880       0.054348       0.060606   

                   Immature B_99  
   ARNTL2_+_(16g)       0.017915  
   ASCL2_+_(20g)        0.023043  
   ATF1_+_(11g)         0.151144  
   ATF5_+_(40g)         0.038348  
   BACH2_-_(355g)       0.100667  
   ...                       ...  
   ZNF749_+_(32g)       0.030064  
   ZNF764_+_(94g)       0.027047  
   ZNF787_+_(12g)       0.056473  
   ZNF823_+_(10g)       0.003510  
   ZNF846_+_(23g)       0.083228  

   [263 rows x 500 columns],
   'Region_based':                   Pro B_0   Pro B_1   Pro B_2   Pro B_3   Pro B_4   Pro B_5  \
   ARNTL2_+_(22r)   0.069249  0.074134  0.106415  0.048688  0.099621  0.095999   
   ASCL2_+_(37r)    0.072238  0.067850  0.108941  0.051727  0.097610  0.103141   
   ATF1_+_(16r)     0.741583  0.742039  0.740695  0.742274  0.741787  0.739226   
   ATF5_+_(51r)     0.023015  0.019451  0.015971  0.023982  0.017605  0.017606   
   BACH2_-_(689r)   0.017710  0.012841  0.007685  0.017712  0.009622  0.013364   
   ...                   ...       ...       ...       ...       ...       ...   
   ZNF749_+_(37r)   0.180894  0.175170  0.175314  0.180327  0.177141  0.172473   
   ZNF764_+_(186r)  0.030028  0.027793  0.028437  0.032387  0.027725  0.025193   
   ZNF787_+_(12r)   0.004398  0.005751  0.005317  0.009135  0.004520  0.003369   
   ZNF823_+_(10r)   0.003212  0.001440  0.005641  0.005034  0.002931  0.000203   
   ZNF846_+_(30r)   0.046822  0.043718  0.044767  0.056588  0.044321  0.037548   

                     Pro B_6   Pro B_7   Pro B_8   Pro B_9  ...  Immature B_90  \
   ARNTL2_+_(22r)   0.035089  0.115269  0.072128  0.055414  ...       0.000033   
   ASCL2_+_(37r)    0.041967  0.114644  0.067850  0.059213  ...       0.007224   
   ATF1_+_(16r)     0.740236  0.739457  0.740866  0.740832  ...       0.744113   
   ATF5_+_(51r)     0.024714  0.014213  0.023645  0.016595  ...       0.015432   
   BACH2_-_(689r)   0.021866  0.007947  0.016768  0.012575  ...       0.015791   
   ...                   ...       ...       ...       ...  ...            ...   
   ZNF749_+_(37r)   0.179455  0.174581  0.180345  0.170786  ...       0.159023   
   ZNF764_+_(186r)  0.029557  0.026516  0.031544  0.025501  ...       0.022454   
   ZNF787_+_(12r)   0.007808  0.002851  0.007064  0.004967  ...       0.003288   
   ZNF823_+_(10r)   0.001548  0.003599  0.003803  0.000183  ...       0.000000   
   ZNF846_+_(30r)   0.053528  0.040813  0.057119  0.036068  ...       0.020250   

                    Immature B_91  Immature B_92  Immature B_93  Immature B_94  \
   ARNTL2_+_(22r)        0.000631       0.004717       0.000709       0.000950   
   ASCL2_+_(37r)         0.007108       0.005848       0.007421       0.007115   
   ATF1_+_(16r)          0.741705       0.728774       0.741968       0.742067   
   ATF5_+_(51r)          0.017767       0.023066       0.013755       0.011336   
   BACH2_-_(689r)        0.018348       0.029075       0.009673       0.006156   
   ...                        ...            ...            ...            ...   
   ZNF749_+_(37r)        0.155502       0.151316       0.150934       0.156340   
   ZNF764_+_(186r)       0.020157       0.023097       0.018448       0.020537   
   ZNF787_+_(12r)        0.001316       0.014995       0.002597       0.001223   
   ZNF823_+_(10r)        0.000000       0.000000       0.000000       0.000062   
   ZNF846_+_(30r)        0.014843       0.012562       0.006043       0.014586   

                    Immature B_95  Immature B_96  Immature B_97  Immature B_98  \
   ARNTL2_+_(22r)        0.001180       0.000622       0.010213       0.001576   
   ASCL2_+_(37r)         0.008029       0.008051       0.016792       0.006968   
   ATF1_+_(16r)          0.743253       0.746332       0.742633       0.738687   
   ATF5_+_(51r)          0.010123       0.010158       0.013886       0.021301   
   BACH2_-_(689r)        0.005013       0.003428       0.010294       0.022866   
   ...                        ...            ...            ...            ...   
   ZNF749_+_(37r)        0.148787       0.149600       0.153160       0.154225   
   ZNF764_+_(186r)       0.018243       0.017115       0.019764       0.019668   
   ZNF787_+_(12r)        0.000000       0.000095       0.001393       0.004375   
   ZNF823_+_(10r)        0.000000       0.000000       0.000000       0.000000   
   ZNF846_+_(30r)        0.008003       0.003868       0.009532       0.014560   

                    Immature B_99  
   ARNTL2_+_(22r)        0.005781  
   ASCL2_+_(37r)         0.014822  
   ATF1_+_(16r)          0.741731  
   ATF5_+_(51r)          0.011712  
   BACH2_-_(689r)        0.006642  
   ...                        ...  
   ZNF749_+_(37r)        0.154946  
   ZNF764_+_(186r)       0.021368  
   ZNF787_+_(12r)        0.002187  
   ZNF823_+_(10r)        0.001275  
   ZNF846_+_(30r)        0.016294  

   [263 rows x 500 columns]}}}
SeppeDeWinter commented 6 months ago

Hi @hanapac

Looks like a lot of zero's in your gene expression based pseudobulk matrix.

Can you show


to_show = [
   x.split("_")[0] for x in 
   scplus_obj.uns["Pseudobulk"]["GEX_cell_type"]["eRegulon_AUC_filtered"]["gene_based"]
]

scplus_obj.uns["Pseudobulk"]["GEX_cell_type"]["expression"].loc[to_show]
hanapac commented 5 months ago

Hi @SeppeDeWinter

Thank you for you response. my colleague helped me to resolve this issue, I had to install pandas version 1.5 instead of 2.0.3