In [1]:
# Parameters
sample_name = "KDNY;P0;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_222-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_222-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.
2019-07-23 02:32:09,351 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typekidney (P0)
    Cell GroupOther Tissues
    Experiment NameDHS
    Experiment GroupENCODE
    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
    rep12666601872087.6326168465251NANANANANANA
    rep23316662271567.3972178440198NANANANANANA
    Modelling Metadata
    MetricValue
    auPRC0.628
    Calibrated Recall at 50% FDR0.242
    Number of Positive Examples in Test Data162348
    Number of Negative Examples in Test Data1838873
    Imbalance Ratio in Test Data0.0811
    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
Ctcf
Pbx3
Hoxc9
Rest
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Tcfecabsent
Fosabsent
Mbtps2absent
Ets1absent
Smarcc2absent
Klf16absent
Foxp4absent
Rfx1absent
Mef2aabsent
Irf1absent
Nfiaabsent
Hsf1absent
Sp3absent
9430076C15Rikabsent
Hnf4gabsent
Figlaabsent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Zfp143absent
Egr3absent
Sp2absent
Gabpaabsent
Ascl2absent
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_222-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_222-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_222-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 22952, Positive for: KDNY;P0;D;En
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_222-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_222-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_222-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 21, # seqlets: 6177, Negative for: KDNY;P0;D;En
  • pattern_0: # seqlets: 2077 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1174 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1126 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zic5, Glis3, Gli3, Zic4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 376 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr1h2, Nr6a1, Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 177 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 144 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 126 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 98 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata1, Gata2, Gata6, Mecom

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Figla, Tcfap4, Atoh8, Tcf12, Olig3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 30 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores