Cannot build netwrok from sparseDaiblo - extract correlation between variables

I run a sparseDiablo following the tutorial.
I am really interested in extracting the correlation between the relevant variables and I use the network function to do that.

I use then
net_df<-my.network$M_micr_prot %>% as.data.frame()
To extract the values.
However I get an error on the network function:

> network(sgccda.res, blocks = c(1,2),
+         color.node = c('darkorchid','lightgreen'), cutoff = 0.9,
+         multiple = T, hyper = T, directed = F, loops = F, bipartite = T)
Error in matrix(0, ncol = n, nrow = n) : 
  invalid 'nrow' value (too large or NA)

Any idea how to improve this?
I would also be happy if I could just extract all the correlation and then manipulate them in R.
Thank you

hi @sromano,

It doesn’t seem like that you are using the mixOmics network function. Please use mixOmics::network function and see ?mixOmics::network for examples and arguments.

Hope it helps,

Al

1 Like

You are totally right, I did not realize I had another package with a similar function loaded.
Thank you and sorry for the naive question.

On another note, is there any resource I could use to understand what is the difference between the correlation obtained from the function circosPlot and network. With the first, I realized that the correlation of a variable with itself is not 1. So, I am a bit confused.

Thank you!