# Parameters
data_name = "Muscle;A;CL"
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_55-naivegw"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_55-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 18:51:55,305 [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	Muscle
Cell Group	Other Tissues
Experiment Name	ATAC
Experiment Group	Casellas Lab

Metric	Value
auPRC	0.6301
Calibrated Recall at 50% FDR	0.212
Number of Positive Examples in Test Data	69117
Number of Negative Examples in Test Data	8001734
Imbalance Ratio in Test Data	0.0086
Test Chromosomes	chr2, chr3, chr19

Pattern Name	TF Name(s)	Modisco
metacluster_1/pattern_0 # seqlets: 2311 SequenceContrib ScoresHyp_Contrib Scores	Ctcfl, Ctcf
metacluster_1/pattern_1 # seqlets: 1907 SequenceContrib ScoresHyp_Contrib Scores	Mef2d, Mef2a, Mef2c
metacluster_1/pattern_2 # seqlets: 1780 SequenceContrib ScoresHyp_Contrib Scores	Sp2, Sp3, Klf3, Klf6, Klf1, Sp4, Sp1, Egr1, Klf7, Klf4, E2f4, Klf8, Klf12, Zbtb17, Zfx, Klf5, Zfp281, Wt1, Klf15, Egr2, E2f1, Maz, Sp5, Zbtb1, E2f7, Zfp740
metacluster_1/pattern_3 # seqlets: 1703 SequenceContrib ScoresHyp_Contrib Scores	Six2, Six1, Six4
metacluster_1/pattern_4 # seqlets: 1624 SequenceContrib ScoresHyp_Contrib Scores	Nfib, Nfia, Nfic
metacluster_1/pattern_5 # seqlets: 1457 SequenceContrib ScoresHyp_Contrib Scores	Nfyb, Nfya, Nfyc, Foxi1, Pbx3
metacluster_1/pattern_6 # seqlets: 1396 SequenceContrib ScoresHyp_Contrib Scores	Gabpa, Fli1, Ets1, Elk4, Elk3, Elf1, Erg, Elk1, Etv4, Etv1, Etv5, Etv2, Fev, Etv6, Etv3, XP_911724.4, Ehf, Elf4, Elf5, Spi1, Elf2, Elf3, Spdef, Spib, Irf8, Spic, Prdm1
metacluster_1/pattern_7 # seqlets: 1344 SequenceContrib ScoresHyp_Contrib Scores	Creb1, Atf1, Crem, Tfe3, Creb5, Atf7, Jdp2, Atf2, Srebf1, Tfec, Usf1, Tfeb, Rxrb, Arntl, Mitf, Bhlhe40, Mlx, Srebf2, Usf2, Clock, Xbp1, Creb3l2, Tef, Atf3, Mafb, Npas2, Nfil3, Jun
metacluster_1/pattern_8 # seqlets: 1173 SequenceContrib ScoresHyp_Contrib Scores	Nhlh1, Ptf1a
metacluster_1/pattern_9 # seqlets: 1134 SequenceContrib ScoresHyp_Contrib Scores	Nrf1
metacluster_1/pattern_10 # seqlets: 760 SequenceContrib ScoresHyp_Contrib Scores	Taf1, Yy1, Rfx1, Zfp42, Mxi1
metacluster_1/pattern_11 # seqlets: 571 SequenceContrib ScoresHyp_Contrib Scores	Hlf, Dbp, Cebpb, Cebpd, Cebpa, Cebpg, Cebpe, Ddit3, Atf4, Pou5f1, Sox2, Nanog, Gmeb2
metacluster_1/pattern_12 # seqlets: 532 SequenceContrib ScoresHyp_Contrib Scores	Thap11, Zfp143, Tbx2
metacluster_1/pattern_13 # seqlets: 523 SequenceContrib ScoresHyp_Contrib Scores	Fosl2, Mafk, Mafg, Maf, Maff, Fos, Fosl1, Bach2, Mafa, Fosb, Jund, Junb, Nfe2l2, Nfe2, Batf, Bach1
metacluster_1/pattern_14 # seqlets: 476 SequenceContrib ScoresHyp_Contrib Scores	Ar, Nr3c1, Pgr, Esr1, Esr2
metacluster_1/pattern_15 # seqlets: 352 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_16 # seqlets: 333 SequenceContrib ScoresHyp_Contrib Scores	Ascl2, Myod1, Tal1, Tcf12, Myog, Myf5, Ascl1, Myf6, Tcf3, Tcf21, Tgif1, Bhlha15, Atoh1, Neurod1, Neurod2, Meis2, Tcf7l1, Olig2, Neurog2, Snai2, Meis3, Nhlh2, Pknox2
metacluster_1/pattern_17 # seqlets: 214 SequenceContrib ScoresHyp_Contrib Scores	E2f3
metacluster_1/pattern_18 # seqlets: 196 SequenceContrib ScoresHyp_Contrib Scores	Zbtb33
metacluster_1/pattern_19 # seqlets: 175 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_20 # seqlets: 139 SequenceContrib ScoresHyp_Contrib Scores	Irf1, Irf2, Irf7, Stat2, Irf4, Irf9, Stat1, Irf5, Irf3, Irf6
metacluster_1/pattern_21 # seqlets: 120 SequenceContrib ScoresHyp_Contrib Scores	Nr2f6, Nr4a2, Rxra, Rara, Rarb, Nr2f1, Rarg, Pparg, Ppara, Nr2c2, Nr2f2, Nr2c1, Nr5a2, Esrrg, Nr1h3, Nr4a1, Esrra, Nr2e1, Esrrb, Nr2e3, Nr1i2, Tcf7, Hnf4g, Rxrg
metacluster_1/pattern_22 # seqlets: 83 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_23 # seqlets: 45 SequenceContrib ScoresHyp_Contrib Scores	E2f6, Mbd2
metacluster_1/pattern_24 # seqlets: 37 SequenceContrib ScoresHyp_Contrib Scores	Rfx2, Rfx3, Rfx6, Rfx7, Rfx4