# Parameters
data_name = "immatureB_SPLND;CD43-_CD11b-;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
tomtom_report_root = "http://mitra.stanford.edu/kundaje/msharmin/report/tomtom_outs/cells"
task_dir = "task_242-naivegw"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_242-naivegw/NaiveauPRC.txt"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"
reportfile = "/mnt/lab_data/kundaje/msharmin/annotations/filtering samples_MS2.xlsx"
sheetname = "filter23"

from matlas.reports import display_metadata

load data from labcluster

Using TensorFlow backend.
2019-08-30 19:34:47,506 [WARNING] git-lfs not installed

display_metadata(data_name, perf_file, reportfile, sheetname)

from matlas.reports import display_paiwise_pattern_comparison
from matlas.reports import display_denovo_patterns

display_denovo_patterns(data_name, modisco_root=modisco_root)

TF-MoDISco is using the TensorFlow backend.

display_paiwise_pattern_comparison(data_name, modisco_root, homer_root)

MetaData Name	Description
Cell type	mouse spleen B cells, CD43-,CD11b- (immature B cells)
Cell Group	B cells
Experiment Name	DHS
Experiment Group	ENCODE

replicate	Naïve overlap peaks	IDR peaks	TSS enrichment (< 8 is very poor <10 is low)	Final number of unique mapping, dup-filtered, chrM filtered reads	Number of reads in called peak regions	Fraction of reads in called peak regions	Number of reads in promoter regions	Fraction of reads in promoter regions	Number of reads in enhancer regions	Fraction of reads in enhancer regions
rep1	128596	95629	7.0455	180923266	NA	NA	NA	NA	NA	NA
rep2	128596	95629	17.3411	22166102	4075310	0.184	3084550	0.1393	7952677	0.3591
rep3	128596	95629	13.7848	26076648	4512348	0.1732	3563439	0.1367	9460004	0.363
rep4	128596	95629	18.6816	24991902	6075672	0.2433	4463929	0.1787	9141605	0.366

Metric	Value
auPRC	0.6259
Calibrated Recall at 50% FDR	0.198
Number of Positive Examples in Test Data	107961
Number of Negative Examples in Test Data	7962890
Imbalance Ratio in Test Data	0.0134
Test Chromosomes	chr2, chr3, chr19

Pattern Name	TF Name(s)	Modisco
metacluster_1/pattern_0 # seqlets: 14582 SequenceContrib ScoresHyp_Contrib Scores	Ctcf, Ctcfl
metacluster_1/pattern_1 # seqlets: 2916 SequenceContrib ScoresHyp_Contrib Scores	Spib, Irf8, Irf4, Spi1, Irf2, Irf1, Prdm1, Irf3, Elf5, Elf3, Spic, Stat1, Ets1, Ehf, Stat2, Zscan10, Etv2, Etv4, Etv6, Gabpa, Irf7, Erg, Elf1, Elk1, Elf4, Zkscan5, Elf2, Etv3, Fli1, XP_911724.4, Bcl6
metacluster_1/pattern_2 # seqlets: 1801 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_3 # seqlets: 536 SequenceContrib ScoresHyp_Contrib Scores	Zfp143, Thap11, Tbx2
metacluster_1/pattern_4 # seqlets: 95 SequenceContrib ScoresHyp_Contrib Scores	Nrf1, Sp2, Sp3, Zfx, Sp1, Klf3
metacluster_1/pattern_5 # seqlets: 70 SequenceContrib ScoresHyp_Contrib Scores	Rest