In [3]:
from matlas.matches import DenovoModisco, DenovoHomer
from vdom.helpers import (b, summary)
from IPython.display import display
import numpy as np


def display_paiwise_pattern_comparison(task_idx, sample_name, modiscodir, homerdir):
    display(summary(b(sample_name + " (differential regions)")))
    
    homer_ob = DenovoHomer(homerdir)
#     homer_ob.fetch_tomtom_matches(save_report=True, 
#                                   tomtom_dir= "{0}/{1}_tomtomout".format(homerdir, "CISBP_2.00"))
    homer_ob.load_matched_motifs()
    homer_ob.get_motif_per_celltype()

    modisco_ob = DenovoModisco(modiscodir)
    modisco_ob.load_matched_motifs()
    modisco_ob.get_motif_per_celltype()

    modisco_ob.display_pairwise_tf_table(homer_ob)
    return None

def display_denovo_patterns(sample_name, modiscodir, match_threshold=0.05):
    display(summary(b(sample_name)))
    
    ob = DenovoModisco(modiscodir)
    
    ob.load_matched_motifs()
    ob.get_motif_per_celltype(match_threshold=match_threshold)
    ob.display_individual_table()
    
    return None
In [11]:
root = "/mnt/lab_data/kundaje/users/msharmin/NSC_ATAC_PEAKS_to_share"
task_idx = 8
sample_name = 'aNSC_Young'

display_denovo_patterns(
    sample_name,
    modiscodir="{0}/gw_modisco/multi_tasks/{1}".format(root, sample_name)
)
aNSC_Young
The following two links show list of Denovo Patterns and corresponding Motifs discovered by TF-MoDISco
Click here for Denovo Patterns by TF-MoDISco: #3
Pattern NameTF Name(s)Modisco
metacluster_1/pattern_0 # seqlets: 73 SequenceContrib ScoresHyp_Contrib Scores
Sp2, Sp3, Sp1, Klf3, Sp4, Sp5, Klf6, Wt1, Klf1, Maz,

Zbtb17, Klf15, Egr1, Klf5, Zfx, Zfp281, Rela, Klf4, Egr2, Klf7, E2f4,

Klf8, Klf12, Usf2, Mxi1, E2f1, Sall4, Nr1h4, Srebf2, Fli1, Ctcfl, E2f7,

Egr3, Ptf1a
metacluster_1/pattern_1 # seqlets: 68 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_2 # seqlets: 55 SequenceContrib ScoresHyp_Contrib Scores
Ctcf
Click here for Motifs by TF-MoDISco: #35
TF NamePattern(s)
Sp2
Pattern NameModiscoSignificance
metacluster_1/pattern_04.1162800000000005e-14
metacluster_1/pattern_14.1162800000000005e-14
Sp3
Pattern NameModiscoSignificance
metacluster_1/pattern_02.07019e-12
metacluster_1/pattern_12.07019e-12
Sp1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.000345329
metacluster_1/pattern_10.000345329
Klf3
Pattern NameModiscoSignificance
metacluster_1/pattern_04.1517100000000003e-10
metacluster_1/pattern_14.1517100000000003e-10
Sp4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00239199
metacluster_1/pattern_10.00239199
Sp5
Pattern NameModiscoSignificance
metacluster_1/pattern_03.4545400000000004e-08
metacluster_1/pattern_13.4545400000000004e-08
Klf6
Pattern NameModiscoSignificance
metacluster_1/pattern_06.621460000000001e-07
metacluster_1/pattern_16.621460000000001e-07
Wt1
Pattern NameModiscoSignificance
metacluster_1/pattern_02.8132799999999997e-06
metacluster_1/pattern_12.8132799999999997e-06
Klf1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.04921930000000001
metacluster_1/pattern_10.04921930000000001
Maz
Pattern NameModiscoSignificance
metacluster_1/pattern_08.91648e-06
metacluster_1/pattern_18.91648e-06
Zbtb17
Pattern NameModiscoSignificance
metacluster_1/pattern_01.43825e-05
metacluster_1/pattern_11.43825e-05
Klf15
Pattern NameModiscoSignificance
metacluster_1/pattern_02.45751e-05
metacluster_1/pattern_12.45751e-05
Egr1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00658342
metacluster_1/pattern_10.00658342
Klf5
Pattern NameModiscoSignificance
metacluster_1/pattern_00.000214592
metacluster_1/pattern_10.000214592
Zfx
Pattern NameModiscoSignificance
metacluster_1/pattern_00.013394999999999999
metacluster_1/pattern_10.013394999999999999
Zfp281
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00036799099999999997
metacluster_1/pattern_10.00036799099999999997
Rela
Pattern NameModiscoSignificance
metacluster_1/pattern_00.000507873
metacluster_1/pattern_10.000507873
Klf4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00141622
metacluster_1/pattern_10.00141622
Egr2
Pattern NameModiscoSignificance
metacluster_1/pattern_00.047066500000000004
metacluster_1/pattern_10.047066500000000004
Klf7
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00106936
metacluster_1/pattern_10.00106936
E2f4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00121524
metacluster_1/pattern_10.00121524
Klf8
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00228068
metacluster_1/pattern_10.00228068
Klf12
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00262097
metacluster_1/pattern_10.00262097
Usf2
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00787577
metacluster_1/pattern_10.00787577
Mxi1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.0133511
metacluster_1/pattern_10.0133511
E2f1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.013394999999999999
metacluster_1/pattern_10.013394999999999999
Sall4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.0367592
metacluster_1/pattern_10.0367592
Nr1h4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.0385269
metacluster_1/pattern_10.0385269
Srebf2
Pattern NameModiscoSignificance
metacluster_1/pattern_00.044988400000000005
metacluster_1/pattern_10.044988400000000005
Fli1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.047066500000000004
metacluster_1/pattern_10.047066500000000004
Ctcfl
Pattern NameModiscoSignificance
metacluster_1/pattern_00.048119300000000004
metacluster_1/pattern_10.048119300000000004
metacluster_1/pattern_22.3222099999999997e-08
E2f7
Pattern NameModiscoSignificance
metacluster_1/pattern_00.04921930000000001
metacluster_1/pattern_10.04921930000000001
Egr3
Pattern NameModiscoSignificance
metacluster_1/pattern_00.04921930000000001
metacluster_1/pattern_10.04921930000000001
Ptf1a
Pattern NameModiscoSignificance
metacluster_1/pattern_00.04926919999999999
metacluster_1/pattern_10.04926919999999999
Ctcf
Pattern NameModiscoSignificance
metacluster_1/pattern_22.13124e-11
In [4]:
root = "/mnt/lab_data/kundaje/users/msharmin/NSC_ATAC_PEAKS_to_share"
task_idx = 8
sample_name = 'aNSC_Young'

display_paiwise_pattern_comparison(
    task_idx, sample_name, 
    modiscodir="{0}/gw_modisco/multi_tasks/{1}".format(root, sample_name),
    homerdir="{0}/gw_homer/{1}".format(root, sample_name),
)
aNSC_Young (differential regions)
Number of CISBP TFs obtained by TF-MoDISco and Homer
Shared TFs between TF-MoDISco and Homer: #6
TF NameModiscoHomer
Sall4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.0367592
metacluster_1/pattern_10.0367592
Pattern NameHomerSignificance
motif24.motif0.025212900000000003
Egr2
Pattern NameModiscoSignificance
metacluster_1/pattern_00.047066500000000004
metacluster_1/pattern_10.047066500000000004
Pattern NameHomerSignificance
motif24.motif0.00907194
Zbtb17
Pattern NameModiscoSignificance
metacluster_1/pattern_01.43825e-05
metacluster_1/pattern_11.43825e-05
Pattern NameHomerSignificance
motif24.motif0.00876961
Sp1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.000345329
metacluster_1/pattern_10.000345329
Pattern NameHomerSignificance
motif24.motif0.0430356
Maz
Pattern NameModiscoSignificance
metacluster_1/pattern_08.91648e-06
metacluster_1/pattern_18.91648e-06
Pattern NameHomerSignificance
motif24.motif0.025212900000000003
Zfp281
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00036799099999999997
metacluster_1/pattern_10.00036799099999999997
Pattern NameHomerSignificance
motif24.motif0.028761900000000003
Unique TF-MoDISco TFs: #29
TF NameModiscoHomer
Klf8
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00228068
metacluster_1/pattern_10.00228068
Absent
Rela
Pattern NameModiscoSignificance
metacluster_1/pattern_00.000507873
metacluster_1/pattern_10.000507873
Absent
Klf6
Pattern NameModiscoSignificance
metacluster_1/pattern_06.621460000000001e-07
metacluster_1/pattern_16.621460000000001e-07
Absent
Mxi1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.0133511
metacluster_1/pattern_10.0133511
Absent
Klf3
Pattern NameModiscoSignificance
metacluster_1/pattern_04.1517100000000003e-10
metacluster_1/pattern_14.1517100000000003e-10
Absent
Sp2
Pattern NameModiscoSignificance
metacluster_1/pattern_04.1162800000000005e-14
metacluster_1/pattern_14.1162800000000005e-14
Absent
Klf15
Pattern NameModiscoSignificance
metacluster_1/pattern_02.45751e-05
metacluster_1/pattern_12.45751e-05
Absent
Wt1
Pattern NameModiscoSignificance
metacluster_1/pattern_02.8132799999999997e-06
metacluster_1/pattern_12.8132799999999997e-06
Absent
Egr1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00658342
metacluster_1/pattern_10.00658342
Absent
Ctcf
Pattern NameModiscoSignificance
metacluster_1/pattern_22.13124e-11
Absent
Klf7
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00106936
metacluster_1/pattern_10.00106936
Absent
E2f1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.013394999999999999
metacluster_1/pattern_10.013394999999999999
Absent
Ptf1a
Pattern NameModiscoSignificance
metacluster_1/pattern_00.04926919999999999
metacluster_1/pattern_10.04926919999999999
Absent
Sp3
Pattern NameModiscoSignificance
metacluster_1/pattern_02.07019e-12
metacluster_1/pattern_12.07019e-12
Absent
Sp5
Pattern NameModiscoSignificance
metacluster_1/pattern_03.4545400000000004e-08
metacluster_1/pattern_13.4545400000000004e-08
Absent
Klf5
Pattern NameModiscoSignificance
metacluster_1/pattern_00.000214592
metacluster_1/pattern_10.000214592
Absent
Egr3
Pattern NameModiscoSignificance
metacluster_1/pattern_00.04921930000000001
metacluster_1/pattern_10.04921930000000001
Absent
Zfx
Pattern NameModiscoSignificance
metacluster_1/pattern_00.013394999999999999
metacluster_1/pattern_10.013394999999999999
Absent
Srebf2
Pattern NameModiscoSignificance
metacluster_1/pattern_00.044988400000000005
metacluster_1/pattern_10.044988400000000005
Absent
Klf4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00141622
metacluster_1/pattern_10.00141622
Absent
E2f4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00121524
metacluster_1/pattern_10.00121524
Absent
Nr1h4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.0385269
metacluster_1/pattern_10.0385269
Absent
Ctcfl
Pattern NameModiscoSignificance
metacluster_1/pattern_00.048119300000000004
metacluster_1/pattern_10.048119300000000004
metacluster_1/pattern_22.3222099999999997e-08
Absent
Klf1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.04921930000000001
metacluster_1/pattern_10.04921930000000001
Absent
Usf2
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00787577
metacluster_1/pattern_10.00787577
Absent
Sp4
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00239199
metacluster_1/pattern_10.00239199
Absent
Klf12
Pattern NameModiscoSignificance
metacluster_1/pattern_00.00262097
metacluster_1/pattern_10.00262097
Absent
Fli1
Pattern NameModiscoSignificance
metacluster_1/pattern_00.047066500000000004
metacluster_1/pattern_10.047066500000000004
Absent
E2f7
Pattern NameModiscoSignificance
metacluster_1/pattern_00.04921930000000001
metacluster_1/pattern_10.04921930000000001
Absent
Unique Homer TFs: #2
TF NameModiscoHomer
Zfp637Absent
Pattern NameHomerSignificance
motif26.motif0.0110835
Runx3Absent
Pattern NameHomerSignificance
motif12.motif0.032502699999999995
In [ ]: