Module name: nmf-subset

Subset an NMF basis (prey) matrix to only include preys enriched in specified compartments.

parameters	definition	default
abundanceCap	the value to cap cell color on the heat map	1
basisMatrix	NMF basis matrix
clusteringMethod	the hierarchical clustering method	complete
distanceMetric	the distance metric	euclidean
minAbundance	the minimum abundance for limiting the color on the heat map	0
minNMFScore	the minimum score required in any of the specified ranks to include a row	0
outFile	output file name	basis-subset.svg
ranks1	ranks defining first NMF compartment
ranks2	ranks defining second NMF compartment
specificity	the fold-change the ranks of interest must have relative to remaining ranks to be included	2
threshold	fractional threshold (relative to max) to consider a prey enriched in a compartment	0.5

Example file formats

basisMatrix

variable,1,2,3
AAAS,0.0,0.18373784550412228,0.0
AAK1,0.13963834317658874,0.0,0.0
AAR2,0.0,0.016517285371126216,0.034697999230769466
AARS2,0.0,0.0,0.001598769548285137

Output

• heat map as svg
• legend for fold enrichment