README
¶
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
Documentation
Source Files
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