convert2cytoscape: Convert Adjacency Matrix to Cytoscape Format

Description Usage Arguments Value Author(s) Examples

View source: R/convert2cytoscape.R

Description

Converts an adjacency matrix to Cytoscape's sparse matrix format

Usage

1

Arguments

A

A cleaned, finalized response matrix ready to be visualized

Value

A sparse matrix formatted for Cytoscape

Author(s)

Alexander Christensen <[email protected]>

Examples

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#finalize rmatA
finalCmat <- finalize(convmat)
#finalize rmatB
finalRmat <- finalize(rmat)

#equate rmatA and rmatB
eq1 <- equate(finalCmat,finalRmat)

#obtain respective equated response matrices
eqCmat <- eq1$rmatA
eqRmat <- eq1$rmatB

#compute similarity matrix
cosC <- cosine(eqCmat)
cosR <- cosine(eqRmat)

#compute networks using NetworkToolbox
Cnet <- NetworkToolbox::TMFG(cosC)$A
Rnet <- NetworkToolbox::TMFG(cosR)$A

#covert to Cytoscape format
ctyoC <- convert2cytoscape(Cnet)
ctyoR <- convert2cytoscape(Rnet)

AlexChristensen/SemNetToolbox documentation built on Aug. 7, 2018, 6:02 p.m.