matrix

README

Module name: network-matrix

Generate network from a matrix.

parameters	definition	default
colorList	text file with hex colors
cutoff	cutoff for matrix value that should be considered an edge	0.01
localizations	ordered list of all possible localizations
matrix	matrix with genes as rows and localizations as columns
nodeLocalizations	list of primary localizations for genes
outFile	output file with all node pairs and edge weight (correlation)	matrix.txt
outFileNetwork	output file name Cytoscape network	matrix.cyjs

Example file formats

colorList

#C0B9B2
#1CE6FF
#FF4A46
#008941

localization

GO:0005654	nucleoplasm
GO:0005694	chromosome
GO:0005730	nucleolus
GO:0005741	mitochondrial outer membrane
GO:0005743	mitochondrial inner membrane

matrix

gene	GO:0005694	GO:0016604	GO:0005635
AAAS	0.0000	0.0000	0.2500
AAK1	0.0000	0.2200	0.6700

Output

• matrix.cyjs: Cytoscape formatted file with nodes placed on a grid
• matrix.txt: node pairs

Documentation

Overview

Package matrix creates files for visualizing LBA as a correlation network.

Index

• func Network(fileOptions map[string]interface{})

Functions

func Network

func Network(fileOptions map[string]interface{})

Network creates a Cytoscape and txt of node pairs for visualizing a matrix as a network.