search

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.
Other
186 stars 29 forks source link

ctx_results.hdf5 AND dem_results.hdf5, I do not understdand #398

Open w1973145618 opened 6 months ago

w1973145618 commented 6 months ago

Hello, dear Sevan, After running the scenicplus pipeline, I obtained ctx_results.hdf5 AND dem_results.hdf5 result where I generated 25 topics and annotated eight cell types in my work. However, the results in part sctx_results.hdf5 AND dem_results.hdf5 are different. In part ctx_results.hdf5, I obtained results for each topic, while in part AND dem_results.hdf5, only a portion of the topics' results were obtained. I'm not sure what could be the reason for this discrepancy and sincerely hope you can help me clarify this issue.

ctx_results.hdf5

with pd.HDFStore('./outs/ctx_results.hdf5') as store:
    keys = store.keys()
print(len(keys))
print(keys)

116 ['/Topics_top_3k_Topic9/motif_enrichment', '/Topics_top_3k_Topic9/regions_to_db', '/Topics_top_3k_Topic8/motif_enrichment', '/Topics_top_3k_Topic8/regions_to_db', '/Topics_top_3k_Topic7/motif_enrichment', '/Topics_top_3k_Topic7/regions_to_db', '/Topics_top_3k_Topic6/motif_enrichment', '/Topics_top_3k_Topic6/regions_to_db', '/Topics_top_3k_Topic5/motif_enrichment', '/Topics_top_3k_Topic5/regions_to_db', '/Topics_top_3k_Topic4/motif_enrichment', '/Topics_top_3k_Topic4/regions_to_db', '/Topics_top_3k_Topic3/motif_enrichment', '/Topics_top_3k_Topic3/regions_to_db', '/Topics_top_3k_Topic25/motif_enrichment', '/Topics_top_3k_Topic25/regions_to_db', '/Topics_top_3k_Topic24/motif_enrichment', '/Topics_top_3k_Topic24/regions_to_db', '/Topics_top_3k_Topic23/motif_enrichment', '/Topics_top_3k_Topic23/regions_to_db', '/Topics_top_3k_Topic22/motif_enrichment', '/Topics_top_3k_Topic22/regions_to_db', '/Topics_top_3k_Topic21/motif_enrichment', '/Topics_top_3k_Topic21/regions_to_db', '/Topics_top_3k_Topic20/motif_enrichment', '/Topics_top_3k_Topic20/regions_to_db', '/Topics_top_3k_Topic2/motif_enrichment', '/Topics_top_3k_Topic2/regions_to_db', '/Topics_top_3k_Topic19/motif_enrichment', '/Topics_top_3k_Topic19/regions_to_db', '/Topics_top_3k_Topic18/motif_enrichment', '/Topics_top_3k_Topic18/regions_to_db', '/Topics_top_3k_Topic17/motif_enrichment', '/Topics_top_3k_Topic17/regions_to_db', '/Topics_top_3k_Topic16/motif_enrichment', '/Topics_top_3k_Topic16/regions_to_db', '/Topics_top_3k_Topic15/motif_enrichment', '/Topics_top_3k_Topic15/regions_to_db', '/Topics_top_3k_Topic14/motif_enrichment', '/Topics_top_3k_Topic14/regions_to_db', '/Topics_top_3k_Topic13/motif_enrichment', '/Topics_top_3k_Topic13/regions_to_db', '/Topics_top_3k_Topic12/motif_enrichment', '/Topics_top_3k_Topic12/regions_to_db', '/Topics_top_3k_Topic11/motif_enrichment', '/Topics_top_3k_Topic11/regions_to_db', '/Topics_top_3k_Topic10/motif_enrichment', '/Topics_top_3k_Topic10/regions_to_db', '/Topics_top_3k_Topic1/motif_enrichment', '/Topics_top_3k_Topic1/regions_to_db', '/Topics_otsu_Topic9/motif_enrichment', '/Topics_otsu_Topic9/regions_to_db', '/Topics_otsu_Topic8/motif_enrichment', '/Topics_otsu_Topic8/regions_to_db', '/Topics_otsu_Topic7/motif_enrichment', '/Topics_otsu_Topic7/regions_to_db', '/Topics_otsu_Topic6/motif_enrichment', '/Topics_otsu_Topic6/regions_to_db', '/Topics_otsu_Topic5/motif_enrichment', '/Topics_otsu_Topic5/regions_to_db', '/Topics_otsu_Topic4/motif_enrichment', '/Topics_otsu_Topic4/regions_to_db', '/Topics_otsu_Topic3/motif_enrichment', '/Topics_otsu_Topic3/regions_to_db', '/Topics_otsu_Topic25/motif_enrichment', '/Topics_otsu_Topic25/regions_to_db', '/Topics_otsu_Topic24/motif_enrichment', '/Topics_otsu_Topic24/regions_to_db', '/Topics_otsu_Topic23/motif_enrichment', '/Topics_otsu_Topic23/regions_to_db', '/Topics_otsu_Topic22/motif_enrichment', '/Topics_otsu_Topic22/regions_to_db', '/Topics_otsu_Topic21/motif_enrichment', '/Topics_otsu_Topic21/regions_to_db', '/Topics_otsu_Topic20/motif_enrichment', '/Topics_otsu_Topic20/regions_to_db', '/Topics_otsu_Topic2/motif_enrichment', '/Topics_otsu_Topic2/regions_to_db', '/Topics_otsu_Topic19/motif_enrichment', '/Topics_otsu_Topic19/regions_to_db', '/Topics_otsu_Topic18/motif_enrichment', '/Topics_otsu_Topic18/regions_to_db', '/Topics_otsu_Topic17/motif_enrichment', '/Topics_otsu_Topic17/regions_to_db', '/Topics_otsu_Topic16/motif_enrichment', '/Topics_otsu_Topic16/regions_to_db', '/Topics_otsu_Topic15/motif_enrichment', '/Topics_otsu_Topic15/regions_to_db', '/Topics_otsu_Topic14/motif_enrichment', '/Topics_otsu_Topic14/regions_to_db', '/Topics_otsu_Topic13/motif_enrichment', '/Topics_otsu_Topic13/regions_to_db', '/Topics_otsu_Topic12/motif_enrichment', '/Topics_otsu_Topic12/regions_to_db', '/Topics_otsu_Topic11/motif_enrichment', '/Topics_otsu_Topic11/regions_to_db', '/Topics_otsu_Topic10/motif_enrichment', '/Topics_otsu_Topic10/regions_to_db', '/Topics_otsu_Topic1/motif_enrichment', '/Topics_otsu_Topic1/regions_to_db', '/DARs_cell_type_T_cell/motif_enrichment', '/DARs_cell_type_T_cell/regions_to_db', '/DARs_cell_type_Neural/motif_enrichment', '/DARs_cell_type_Neural/regions_to_db', '/DARs_cell_type_Myeloid/motif_enrichment', '/DARs_cell_type_Myeloid/regions_to_db', '/DARs_cell_type_Mescechymal2Epithelial/motif_enrichment', '/DARs_cell_type_Mescechymal2Epithelial/regions_to_db', '/DARs_cell_type_Mescechymal/motif_enrichment', '/DARs_cell_type_Mescechymal/regions_to_db', '/DARs_cell_type_Epithelial/motif_enrichment', '/DARs_cell_type_Epithelial/regions_to_db', '/DARs_cell_type_Endothelial/motif_enrichment', '/DARs_cell_type_Endothelial/regions_to_db', '/DARs_cell_type_B_cell/motif_enrichment', '/DARs_cell_type_B_cell/regions_to_db']

dem_results.hdf5

with pd.HDFStore('./outs/dem_results.hdf5') as store:
    keys = store.keys()
print(len(keys))
print(keys)

58 ['/Topics_top_3k_Topic9_vs_all/motif_enrichment', '/Topics_top_3k_Topic9_vs_all/regions_to_db', '/Topics_top_3k_Topic8_vs_all/motif_enrichment', '/Topics_top_3k_Topic8_vs_all/regions_to_db', '/Topics_top_3k_Topic7_vs_all/motif_enrichment', '/Topics_top_3k_Topic7_vs_all/regions_to_db', '/Topics_top_3k_Topic6_vs_all/motif_enrichment', '/Topics_top_3k_Topic6_vs_all/regions_to_db', '/Topics_top_3k_Topic5_vs_all/motif_enrichment', '/Topics_top_3k_Topic5_vs_all/regions_to_db', '/Topics_top_3k_Topic4_vs_all/motif_enrichment', '/Topics_top_3k_Topic4_vs_all/regions_to_db', '/Topics_top_3k_Topic3_vs_all/motif_enrichment', '/Topics_top_3k_Topic3_vs_all/regions_to_db', '/Topics_top_3k_Topic2_vs_all/motif_enrichment', '/Topics_top_3k_Topic2_vs_all/regions_to_db', '/Topics_top_3k_Topic24_vs_all/motif_enrichment', '/Topics_top_3k_Topic24_vs_all/regions_to_db', '/Topics_top_3k_Topic23_vs_all/motif_enrichment', '/Topics_top_3k_Topic23_vs_all/regions_to_db', '/Topics_top_3k_Topic21_vs_all/motif_enrichment', '/Topics_top_3k_Topic21_vs_all/regions_to_db', '/Topics_top_3k_Topic20_vs_all/motif_enrichment', '/Topics_top_3k_Topic20_vs_all/regions_to_db', '/Topics_top_3k_Topic1_vs_all/motif_enrichment', '/Topics_top_3k_Topic1_vs_all/regions_to_db', '/Topics_top_3k_Topic18_vs_all/motif_enrichment', '/Topics_top_3k_Topic18_vs_all/regions_to_db', '/Topics_top_3k_Topic15_vs_all/motif_enrichment', '/Topics_top_3k_Topic15_vs_all/regions_to_db', '/Topics_top_3k_Topic13_vs_all/motif_enrichment', '/Topics_top_3k_Topic13_vs_all/regions_to_db', '/Topics_top_3k_Topic12_vs_all/motif_enrichment', '/Topics_top_3k_Topic12_vs_all/regions_to_db', '/Topics_otsu_Topic9_vs_all/motif_enrichment', '/Topics_otsu_Topic9_vs_all/regions_to_db', '/Topics_otsu_Topic7_vs_all/motif_enrichment', '/Topics_otsu_Topic7_vs_all/regions_to_db', '/Topics_otsu_Topic6_vs_all/motif_enrichment', '/Topics_otsu_Topic6_vs_all/regions_to_db', '/Topics_otsu_Topic5_vs_all/motif_enrichment', '/Topics_otsu_Topic5_vs_all/regions_to_db', '/Topics_otsu_Topic4_vs_all/motif_enrichment', '/Topics_otsu_Topic4_vs_all/regions_to_db', '/Topics_otsu_Topic2_vs_all/motif_enrichment', '/Topics_otsu_Topic2_vs_all/regions_to_db', '/Topics_otsu_Topic1_vs_all/motif_enrichment', '/Topics_otsu_Topic1_vs_all/regions_to_db', '/Topics_otsu_Topic18_vs_all/motif_enrichment', '/Topics_otsu_Topic18_vs_all/regions_to_db', '/Topics_otsu_Topic15_vs_all/motif_enrichment', '/Topics_otsu_Topic15_vs_all/regions_to_db', '/Topics_otsu_Topic13_vs_all/motif_enrichment', '/Topics_otsu_Topic13_vs_all/regions_to_db', '/DARs_cell_type_T_cell_vs_all/motif_enrichment', '/DARs_cell_type_T_cell_vs_all/regions_to_db', '/DARs_cell_type_Epithelial_vs_all/motif_enrichment', '/DARs_cell_type_Epithelial_vs_all/regions_to_db']

SeppeDeWinter commented 6 months ago

Hi @w1973145618

The reason is that for those topics no enriched motifs were found using DEM.

All the best,

Seppe