Module name: enrichment-heatmap

Creates a heat map visualizing region (domain/motif) fold enrichment (scaled to log2) across NMF or SAFE compartments.

parameters	definition	default
abundanceCap	the value to cap cell color on the heat map	10
clusteringMethod	the hierarchical clustering method	complete
compartmentSummary	files with names defining compartments
distanceMetric	the distance metric	euclidean
enrichmentFile	text file with compartment name and enriched domains/motifs
minAbundance	the minimum abundance for limiting the color on the heat map	0
outFile	output file name	region-heatmap.svg
pValue	pValue cutoff for including a region	0.01

Example file formats

compartmentSummary

rank	term	displayname	go	synonyms	ic
1	[cell junction]	[cell junction]	[GO:0030054]	[]	[1.166]
2	[chromosome]	[chromatin]	[GO:0005694]	"[[chromatid, interphase chromosome, prophase chromosome]]"	[1.256]

enrichmentFile

rank	term	matched	background_size	fold enrichment	pvalue	adj. pvalue	bhfdr	genes
1	PDZ	23	48	8.906	1.62980740014973e-13	4.27009538839229e-11	3.81679389312977e-05	AFDN,CASK,DLG1
1	FERM_C	12	17	13.120	2.1798629399977e-12	2.85562045139698e-10	7.63358778625954e-05	EPB41,EPB41L1,EPB41L2
1	FERM_N	12	18	12.391	6.23068998013292e-12	5.44146924931608e-10	0.000114503816793893	EPB41,EPB41L1,EPB41L2
2	KRAB	24	28	9.905	2.32442462867683e-22	1.02972011050383e-19	2.25733634311512e-05	POGK,RBAK,ZFP1
2	zf-C2H2	30	65	5.333	2.99760216648792e-15	6.63968879877075e-13	4.51467268623025e-05	CTCF,MAZ,PRDM15
2	Bromodomain	13	24	6.259	1.29285132936678e-08	1.70043585864132e-06	6.77200902934537e-05	ATAD2,BPTF,BRD1
2	PWWP	10	14	8.254	1.53538226513889e-08	1.70043585864132e-06	9.0293453724605e-05	BRD1,BRPF3,DNMT3A,GLYR1

Output

• heat map as svg
• legend for fold enrichment