So as a short background, I’m integrating lipidomics and transcriptomics data using rCCA in mixomics. I’ve bought the mixomics book and have been following that very closely. One of the things it recommends is using cytoscape by exporting networks from the rCCA. I can get this to work for every single experimental group comparison with rCCA, except for one. The rCCA completes just fine, and the data looks comparable to any of the other rCCAs, but when I type in the following:
relev.net10 ← network(rCCA10, comp = 1:2, lwd.edge =2, interactive = F,
cutoff = 0.75, plot.graph = F, save = “pdf”, name.save = “rCCA_network10”)
I get the following error:
Error in layout_with_fr(list(1076, FALSE, c(261, 263, 264, 265, 285, 286, :
At vendor/cigraph/src/layout/fruchterman_reingold.c:395 : Weights must be positive for Fruchterman-Reingold layout. Invalid value
I’ve googled this error and the only thing I could find for recommendations would be adjusting the function to be a sum, instead of a max, which I both don’t understand the meaning of as there is no argument I think I can put in to do this, but also am not entirely comfortable doing if this function worked just fine for every other experimental group comparison in rCCA.
Hoping someone else has encountered this error and might have a way around it.
This isn’t anything I’ve run into with any mixomics sample data, and my dataset is far too large to email and a subset of it would very likely not reproduce this error since it’s already looked to be a one off out of the other 8 experimental group comparisons I ran through rCCA.So unfortunately I doubt anyone would be able ot reproduce it. I was more hoping someone could help me understand the error and what could have caused it, considering everything is exactly the same with every other group comparison and rCCA.