In [1]:
# Parameters
sample_name = "Th2_nippo;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_87-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_87-naivegw/NaiveauPRC.txt"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"
In [2]:
from matlas.modisco_report import modisco_report_pipeline, display_metadata
reportfile= "/mnt/lab_data/kundaje/msharmin/mouse_hem/with_tfd/full_mouse50/filtering samples_MS2.xlsx"
sheetname = "filter23"

load data from labcluster

Using TensorFlow backend.
2019-07-22 19:31:27,426 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeTh2 (Nippo infected)
    Cell GroupT cells
    Experiment NameATAC
    Experiment GroupCasellas Lab
    Pipeline Output
    replicateNaïve overlap peaksIDR peaksTSS enrichment (< 8 is very poor <10 is low)Final number of unique mapping, dup-filtered, chrM filtered readsNumber of reads in called peak regionsFraction of reads in called peak regionsNumber of reads in promoter regionsFraction of reads in promoter regionsNumber of reads in enhancer regionsFraction of reads in enhancer regions
    rep112757810150610.223158219367139431860.239690042190.1547200744950.3449
    Modelling Metadata
    MetricValue
    auPRC0.5825
    Calibrated Recall at 50% FDR0.211
    Number of Positive Examples in Test Data112098
    Number of Negative Examples in Test Data7958753
    Imbalance Ratio in Test Data0.0139
    Test Chromosomeschr2, chr3, chr19
In [4]:
from matlas.modisco_report import display_comparative_motif_sets
display_comparative_motif_sets(sample_name, homer_root, modisco_root)

TF-MoDISco is using the TensorFlow backend.
Number of CISBP motifs obtained by TF-MoDISco and Homer-denovo
Shared Motifs
Motif NameModiscoHomer
Smarcc2
Sp2
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Creb1absent
Runx2absent
Rfx3absent
Ergabsent
Irf1absent
Foxi1absent
Rfx1absent
Gata4absent
Relaabsent
Sp3absent
Nfe2absent
Tbpl2absent
Unique Homer Motifs
Motif NameModiscoHomer
Smarcc1absent
Pbx3absent
Relbabsent
Erfabsent
In [5]:
modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=True, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_87-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_87-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_87-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 21397, Positive for: Th2_nippo;A;CL
In [6]:
modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=False, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_87-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_87-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_87-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 27, # seqlets: 13350, Negative for: Th2_nippo;A;CL
  • pattern_0: # seqlets: 3101 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Dbx1, Hmg20b, Lhx3, Tlx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2797 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Glis1, Zbtb7a, Gli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1783 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1110 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 786 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 686 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata3, Gata6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 430 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 389 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ets1, Erg, ENSMUSG00000044690, Spib, Etv6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 358 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 297 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 257 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2, Nfe2l2, Jund, Fos, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 173 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Olig3, Mitf, Tcfe3, Tcfap4, Usf2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 170 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 167 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxa9, Hoxc9, Cdx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 120 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 107 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 90 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143, Tbx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    9430076C15Rik, Atoh1, Srebf1, Hsf1, Creb3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcfec, Srebf1, Usf1, Mitf, Creb3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf2, Klf4, Klf8, Klf7

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Klf6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 35 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores