# Parameters
data_name = "ES;MEF;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_51-naivegw"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_51-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 18:51:06,790 [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	MEFs
Cell Group	ES cells and embryonic tissues
Experiment Name	ATAC
Experiment Group	Casellas Lab

Metric	Value
auPRC	0.6632
Calibrated Recall at 50% FDR	0.192
Number of Positive Examples in Test Data	124907
Number of Negative Examples in Test Data	7945944
Imbalance Ratio in Test Data	0.0155
Test Chromosomes	chr2, chr3, chr19

Pattern Name	TF Name(s)	Modisco
metacluster_1/pattern_0 # seqlets: 3789 SequenceContrib ScoresHyp_Contrib Scores	Junb, Fosl1, Fosb, Fos, Jund, Atf3, Fosl2, Jdp2, Jun, Batf, Bach2, Nfe2, Nfe2l2, Bach1
metacluster_1/pattern_1 # seqlets: 3301 SequenceContrib ScoresHyp_Contrib Scores	Ctcf, Ctcfl
metacluster_1/pattern_2 # seqlets: 2961 SequenceContrib ScoresHyp_Contrib Scores	Klf1, Sp1, Sp3, Sp2, Sp5, Maz, Klf15, Wt1, Klf6, Klf3, Egr1, Sp4, Zbtb17, Zfx, Klf7, Klf4, Egr2, Klf8, Klf12, Zfp281, Klf5, Rela, Fli1, Mxi1, E2f4, E2f3, Usf2, Tfap2c, E2f6, E2f1, Tfap2b, Mbd2, Egr3
metacluster_1/pattern_3 # seqlets: 2013 SequenceContrib ScoresHyp_Contrib Scores	Tead4, Tead2, Tead1
metacluster_1/pattern_4 # seqlets: 1679 SequenceContrib ScoresHyp_Contrib Scores	Erg, Ets1, Elk1, Gabpa, Elk4, Etv2, Etv4, Elf2, Etv5, Elk3, Etv6, Elf1, Spi1, Fev, Etv1, Ehf, Etv3, XP_911724.4, Spib, Elf3, Elf4, Elf5, Irf8, Irf4, Spdef, Spic, Stat4, Ets2
metacluster_1/pattern_5 # seqlets: 1219 SequenceContrib ScoresHyp_Contrib Scores	Atf7, Atf2, Creb5, Creb1, Atf1, Crem, Nfil3, Srebf1, Dbp, Tfec, Cebpa, Cebpb, Mlx, Hlf, Tef, Rxrb, Mafb
metacluster_1/pattern_6 # seqlets: 1031 SequenceContrib ScoresHyp_Contrib Scores	Nfyb, Nfyc, Nfya, Foxi1, Pbx3
metacluster_1/pattern_7 # seqlets: 732 SequenceContrib ScoresHyp_Contrib Scores	Nrf1
metacluster_1/pattern_8 # seqlets: 687 SequenceContrib ScoresHyp_Contrib Scores	Nfib, Nfia, Nfic
metacluster_1/pattern_9 # seqlets: 669 SequenceContrib ScoresHyp_Contrib Scores	Runx1, Runx2, Runx3, Cbfb, Gfi1b
metacluster_1/pattern_10 # seqlets: 476 SequenceContrib ScoresHyp_Contrib Scores	Rfx3, Rfx1, Rfx2, Rfx4, Rfx7, Rfx6, Sox2, Pou5f1
metacluster_1/pattern_11 # seqlets: 373 SequenceContrib ScoresHyp_Contrib Scores	Cebpd, Atf4, Ddit3, Cebpg, Cebpe, Gmeb2
metacluster_1/pattern_12 # seqlets: 347 SequenceContrib ScoresHyp_Contrib Scores	Zfp143, Thap11, Tbx2
metacluster_1/pattern_13 # seqlets: 341 SequenceContrib ScoresHyp_Contrib Scores	Srf
metacluster_1/pattern_14 # seqlets: 295 SequenceContrib ScoresHyp_Contrib Scores	Usf1, Tfeb, Arntl, Mitf, Bhlhe40, Tfe3, Clock, Arnt, Npas2, Srebf2, Creb3l2, Tcfl5, Bhlhe41, Xbp1, Max, Mlxip
metacluster_1/pattern_15 # seqlets: 263 SequenceContrib ScoresHyp_Contrib Scores	Taf1, Yy1, Zfp42
metacluster_1/pattern_16 # seqlets: 244 SequenceContrib ScoresHyp_Contrib Scores	Twist1
metacluster_1/pattern_17 # seqlets: 244 SequenceContrib ScoresHyp_Contrib Scores	Mef2d, Mef2a, Mef2c
metacluster_1/pattern_18 # seqlets: 153 SequenceContrib ScoresHyp_Contrib Scores	Irf1, Irf2, Irf7, Prdm1, Stat1, Irf9, Stat2, Irf5, Irf3, Irf6
metacluster_1/pattern_19 # seqlets: 147 SequenceContrib ScoresHyp_Contrib Scores	Six2, Six1, Six4
metacluster_1/pattern_20 # seqlets: 126 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_21 # seqlets: 86 SequenceContrib ScoresHyp_Contrib Scores	Zbtb33
metacluster_1/pattern_22 # seqlets: 65 SequenceContrib ScoresHyp_Contrib Scores