# Parameters
data_name = "NPC;Ch13;A;GEO"
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_172-naivegw"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_172-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 19:19:40,762 [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	neural progenitor cells(Ch13)
Cell Group	Neural Cells and Tissues
Experiment Name	ATAC
Experiment Group	GEO

Metric	Value
auPRC	0.6109
Calibrated Recall at 50% FDR	0.305
Number of Positive Examples in Test Data	111190
Number of Negative Examples in Test Data	7959661
Imbalance Ratio in Test Data	0.0138
Test Chromosomes	chr2, chr3, chr19

Pattern Name	TF Name(s)	Modisco
metacluster_1/pattern_0 # seqlets: 3554 SequenceContrib ScoresHyp_Contrib Scores	Sp2, Sp3, Sp1, Sp4, Klf3, E2f4, Zbtb17, Klf6, Klf4, Sp5, Egr1, Klf5, Klf7, Wt1, Egr2, Klf12, Klf8, Zfp281, Maz, Klf1, E2f1, Klf15, Srebf2, Egr3, Zfx, Sall4
metacluster_1/pattern_1 # seqlets: 2740 SequenceContrib ScoresHyp_Contrib Scores	Ctcf, Ctcfl
metacluster_1/pattern_2 # seqlets: 1638 SequenceContrib ScoresHyp_Contrib Scores	Nfib, Nfia, Nfic
metacluster_1/pattern_3 # seqlets: 1606 SequenceContrib ScoresHyp_Contrib Scores	Rfx1, Rfx2, Rfx3, Rfx4, Rfx7, Rfx6, Stat4
metacluster_1/pattern_4 # seqlets: 1503 SequenceContrib ScoresHyp_Contrib Scores	Sox3, Sox9, Sox2, Sox17, Sox4, Sox6, Sox12, Nanog, Foxd1, Sry, Sox10
metacluster_1/pattern_5 # seqlets: 1183 SequenceContrib ScoresHyp_Contrib Scores	Nfyb, Nfyc, Nfya, Foxi1, Pbx3
metacluster_1/pattern_6 # seqlets: 1139 SequenceContrib ScoresHyp_Contrib Scores	Atf7, Atf2, Jdp2, Creb1, Creb5, Atf1, Crem, Atf3, Fosl2, Tfec, Srebf1, Creb3l2, Tfe3, Usf1, Mlx, Hlf, Nfil3, Mafb, Fosl1, Dbp, Jun, Tef, Bhlhe40, Rxrb, Usf2, Mitf, Cebpb, Tfeb, Cebpa, Atf4
metacluster_1/pattern_7 # seqlets: 1125 SequenceContrib ScoresHyp_Contrib Scores	Mxi1, Mbd2
metacluster_1/pattern_8 # seqlets: 1067 SequenceContrib ScoresHyp_Contrib Scores	Gabpa, Fli1, Elk1, Elk4, Ets1, Erg, Elk3, Etv5, Fev, Etv4, Elf1, Etv1, Etv6, Etv2, Elf2, Etv3, XP_911724.4, Ehf, Spi1, Elf5, Elf4, Spdef, Elf3, Spib, Spic
metacluster_1/pattern_9 # seqlets: 736 SequenceContrib ScoresHyp_Contrib Scores	Ascl2, Tcf3, Myog, Myod1, Myf6, Nhlh2, Tcf12, Ascl1, Nhlh1, Tcf7l1, Tal1, Ptf1a, Bhlha15, Myf5, Snai2, Tcf4, Atoh1, Tgif1
metacluster_1/pattern_10 # seqlets: 720 SequenceContrib ScoresHyp_Contrib Scores	Nrf1
metacluster_1/pattern_11 # seqlets: 514 SequenceContrib ScoresHyp_Contrib Scores	Fosb, Junb, Fos, Jund, Batf, Bach2, Nfe2l2, Nfe2, Bach1, Mafk, Mafa
metacluster_1/pattern_12 # seqlets: 478 SequenceContrib ScoresHyp_Contrib Scores	Tead2, Tead4, Tead1
metacluster_1/pattern_13 # seqlets: 407 SequenceContrib ScoresHyp_Contrib Scores	Pou2f2, Pou5f1, Pou2f1
metacluster_1/pattern_14 # seqlets: 398 SequenceContrib ScoresHyp_Contrib Scores	Zfp143, Thap11, Tbx2
metacluster_1/pattern_15 # seqlets: 307 SequenceContrib ScoresHyp_Contrib Scores	Taf1, Yy1, Zfp42
metacluster_1/pattern_16 # seqlets: 147 SequenceContrib ScoresHyp_Contrib Scores	Mef2d, Mef2a, Mef2c
metacluster_1/pattern_17 # seqlets: 140 SequenceContrib ScoresHyp_Contrib Scores	Snai1, Zeb1, Meis2
metacluster_1/pattern_18 # seqlets: 64 SequenceContrib ScoresHyp_Contrib Scores	Zbtb33
metacluster_1/pattern_19 # seqlets: 55 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_20 # seqlets: 49 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_21 # seqlets: 49 SequenceContrib ScoresHyp_Contrib Scores	Rest