Re: [igraph] Error in igraph trying to plot a co-ocurrence network

[Tamas Nepusz]

Hi,

The plot_network() function is not part of igraph so we cannot help here. Please contact the authors of the package that implements the plot_network() function for help -- I suspect that the function is part of the phyloseq package.

T.

On Fri, Jun 9, 2017 at 1:29 PM, Miguel Angel Fernández Martínez <address@hidden> wrote:

Hi there!

I am very very new at igraph package and just a little more than a rookie in R, so maybe my questions are a bit trivial. I apologize for that.

I am triying to run a script that combines the package 'Spiec-Easi' with 'igraph' to perform a netwowork analysis and its plot.

I have encountered some problems with my data format, but most of them has been overcome. However, I am now facing one that I cannot solve by myself. I copy my whole script and I attach the data in .csv file format just in case you want to have a look at it:

library(devtools)
library(SpiecEasi)
library(igraph)
library(phyloseq)

tabla <- read.csv("tabla_prueba.txt")

rownames(tabla) <- tabla[,1]
tabla <- tabla[,-1]
tabla <- t(tabla)

se.tabla <- spiec.easi(tabla, method='mb', lambda.min.ratio=1e-2, nlambda=20, icov.select.params=list(rep.num=20))

se.tabla <- unlist(se.tabla)

ig.tabla <- adj2igraph(se.tabla$refit)

plot_network(ig.tabla, tabla)

Everything seems to work properly until the very last command, when I get the following:

Error in `$<-.data.frame`(`*tmp*`, "id", value = c(1L, 0L)) : 
  replacement has 2 rows, data has 0

Although it seems to be a very common issue, I have not found any viable solution on Internet.

Can anyone help with this problem?

Thanks a lot!

--
Miguel Ángel Fernández Martínez
PostDoctoral Researcher
Dept. Evolución Molecular, Despacho 10
Tlf.: 91 520 64 33 - Ext. 5415
Centro de Astrobiología (CAB), INTA-CSIC
Madrid, Spain

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