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 gridmatrix.txt: node pairs
Documentation
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