tsnecytoscape

README

Module name: network-tsnecytoscape

Convert a tSNE coordinate system into a .cyjs file for Cytoscape

parameters	definition	default
colorList	text file with hex colors
localizations	ordered list of all possible localizations
nodeCoordinates	text file with list of nodes and x, y coordinates
nodeLocalizations	list of primary localizations for genes
outFile	output file name	map.cyjs
width	the ideal width for the map	1000

Example file formats

colorList

#C0B9B2
#1CE6FF
#FF4A46
#008941

nodeCoordinates

gene	x	y
AAAS	68.5533816047702	-33.9816908466039
AAK1	-28.8672128420763	-43.6402491976645
AAR2	2.2808526181511	-6.97152015675554
AARS2	89.5765051986436	67.0643311315994
AASDH	8.41236940140679	35.7167588576447
AASS	-70.8218291970252	64.4050187741019
AATF	-15.8239071660148	51.4522241800074
ABCA3	-19.8932838810909	-3.05943018550193
ABCB1	-16.1846453937935	91.5103672699896
ABCB10	-52.4758726133164	73.6495265978388

nodeLocalizations

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

### Output
* `map.cyjs`: map in .cyjs format for Cytoscape

Documentation

Overview

Package tsnecytoscape generates a Cytoscape network from t-SNE coordinates.

Index

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

Functions

func Create

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

Create generates a .cyjs file from t-SNE coordinates.