outputgephi | R Documentation |
use the phylsoeq object and cor matrix building Gephi input network file contain edge and node
outputgephi(ps = ps, cor = cor)
ps |
phyloseq abject |
cor |
Correlation matrix |
result2 Which contains 2 lists.Result2[[1]], consists of OTU and its corresponding coordinates. Result2[[2]], consists of the network center coordinates of each group
Contact: Tao Wen 2018203048@njau.edu.cn Jun Yuan junyuan@njau.edu.cn Penghao Xie 2019103106@njau.edu.cn
Yuan J, Zhao J, Wen T, Zhao M, Li R, Goossens P, Huang Q, Bai Y, Vivanco JM, Kowalchuk GA, Berendsen RL, Shen Q Root exudates drive the soil-borne legacy of aboveground pathogen infection Microbiome 2018,DOI: doi: 10.1186/s40168-018-0537-x
data(ps)
result = corMicro (ps = ps,N = 0.02,r.threshold=0.8,p.threshold=0.05,method = "pearson")
#Extract correlation matrix
cor = result[[1]]
gephi <- outputgephi(ps = result[[3]],cor = cor)
edge_Gephi <- gephi[[1]]
head(edge_Gephi)
node_Gephi <- gephi[[2]]
head(node_Gephi)
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