Empty region_to_gene_importances and region_to_gene_correlation when run_scenicplus

[YaoLi3]

Dear team,

I found out that I kept getting empty dictionaries for region_to_gene_importances and region_to_gene_correlation in function calculate_regions_to_genes_relationships.

This is how my scplus_obj looks so far:

>>> scplus_obj
SCENIC+ object with n_cells x n_genes = 380 x 27301 and n_cells x n_regions = 380 x 13303
	metadata_regions:'Chromosome', 'Start', 'End', 'Width', 'cisTopic_nr_frag', 'cisTopic_log_nr_frag', 'cisTopic_nr_acc', 'cisTopic_log_nr_acc'
	metadata_genes:'gene', 'HumanSymbol', 'ZebrafishSymbol', 'MedakaSymbol'
	metadata_cell:'celltype'
	menr:'CTX_topics_otsu_All', 'CTX_topics_otsu_No_promoters', 'DEM_topics_otsu_All', 'DEM_topics_otsu_No_promoters', 'CTX_DARs_region_bin_topics_top3k_All', 'CTX_DARs_region_bin_topics_top3k_No_promoters', 'DEM_DARs_region_bin_topics_top3k_All', 'DEM_DARs_region_bin_topics_top3k_No_promoters', 'CTX_DARs_markers_dict_All', 'CTX_DARs_markers_dict_No_promoters', 'DEM_DARs_markers_dict_All', 'DEM_DARs_markers_dict_No_promoters'

uns keys I managed to obtain:

>>> scplus_obj.uns.keys()
dict_keys(['search_space', 'Cistromes'])

>>> print(list(signatures.keys())[0:5])
['EPAS1_(2r)__CTX_topics_otsu_All__Topic1', 'GATA3_extended_(2r)__CTX_topics_otsu_All__Topic1', 'CEBPA_extended_(5r)__CTX_topics_otsu_All__Topic1', 'AHRR_extended_(2r)__CTX_topics_otsu_All__Topic1', 'EPAS1_extended_(2r)__CTX_topics_otsu_All__Topic1']

>>> scplus_obj.metadata_regions['Chromosome']
NC_018546.1:5882-6382          NC_018546.1
NC_018546.1:13199-13699        NC_018546.1
NC_018546.1:8630-9130          NC_018546.1
NC_018546.1:16189-16689        NC_018546.1
NC_018546.1:2799-3299          NC_018546.1
                                 ...      
NW_023419892.1:1214-1714    NW_023419892.1
NW_023420775.1:1304-1804    NW_023420775.1
NW_023422538.1:881-1381     NW_023422538.1
NW_023423559.1:590-1090     NW_023423559.1
NW_023424523.1:95-595       NW_023424523.1
Name: Chromosome, Length: 13303, dtype: object

search space and Cistromes:

>>> scplus_obj.uns['search_space']
                          Name                       Gene Distance
0          NC_018546.1:413-913  unassigned_transcript_779      [0]
1          NC_018546.1:413-913  unassigned_transcript_780    [348]
2        NC_018546.1:1486-1986  unassigned_transcript_781      [0]
3        NC_018546.1:2027-2527  unassigned_transcript_781      [0]
4         NC_018546.1:923-1423  unassigned_transcript_781      [0]
...                        ...                        ...      ...
2110  NW_023418709.1:3192-3692             XR_004947600.1   [1662]
2111  NW_023418725.1:3081-3581             XM_036211287.1      [0]
2112  NW_023419487.1:1261-1761             XM_024261841.2     [58]
2113    NW_023419487.1:154-654             XM_024261841.2   [1165]
2114   NW_023423559.1:590-1090             XM_024261831.1      [0]

[2115 rows x 3 columns]

>>> scplus_obj.uns['Cistromes']
{'Unfiltered': {'ASCL1_(14r)': +----------------+-----------+-----------+
| Chromosome     | Start     | End       |
| (category)     | (int64)   | (int64)   |
|----------------+-----------+-----------|
| NC_050516.1    | 15666009  | 15666509  |
| NC_050522.1    | 24706071  | 24706571  |
| NC_050524.1    | 33821116  | 33821616  |
| NC_050526.1    | 15299260  | 15299760  |
| ...            | ...       | ...       |
| NW_023416925.1 | 96474     | 96974     |
| NW_023417048.1 | 48904     | 49404     |
| NW_023417060.1 | 17959     | 18459     |
| NW_023417405.1 | 72        | 572       |
+----------------+-----------+-----------+
Unstranded PyRanges object has 14 rows and 3 columns from 14 chromosomes.
For printing, the PyRanges was sorted on Chromosome.

>>> len(scplus_obj.uns['Cistromes']['Unfiltered'])
59

Before calculate_regions_to_genes_relationships:
At first I was running get_search_space on all default parameters, and end up getting negative Start positions (which doesn't make sense) and negative Distances. (By the way, it seems like users will not be warned when negative numbers occur and no code are handling this situation. Indeed, users should pass in upstream/downstream range according to their target species genome size, but lots of people like to run software on default first, and in some rare cases, this could happen)

---------------------search_space---------------------
                          Name                       Gene Distance
0          NC_018546.1:413-913  unassigned_transcript_778   [-594]
1         NC_018546.1:923-1423  unassigned_transcript_778  [-1104]
2          NC_018546.1:413-913  unassigned_transcript_779      [0]
3         NC_018546.1:923-1423  unassigned_transcript_779   [-163]
4        NC_018546.1:1486-1986  unassigned_transcript_780   [-654]
...                        ...                        ...      ...
3329   NW_023419278.1:838-1338             XM_024264679.1   [-361]
3330  NW_023419487.1:1261-1761             XM_024261841.2     [58]
3331    NW_023419487.1:154-654             XM_024261841.2   [1165]
3332   NW_023423559.1:590-1090             XM_024261831.1      [0]
3333     NW_023424523.1:95-595             XR_002917844.2   [-148]

[3334 rows x 3 columns]

What I have done:

1. set use_gene_boundaries to True;
2. set upstream and downstream to very small numbers. Still getting negative Start_b at this point;
3. turn negative Start_b into 0;
4. filter out regions_per_gene that has negative Distance;

Still have all empty region_to_gene_importances and region_to_gene_correlation.

Any help will be much appreciated!

Thanks in advance,
Yao