gap between edges and nodes on plot

[dheadl]

Hello,

Thank you for this great package!

I am trying to plot a network comparison but there is a gap between the nodes and the edges. If I change the netConstruct to include "filtTax = "highestVar",
filtTaxPar = list(highestVar = 50)"
this does not happen. Is there a way to stop this gap from happening apart from reducing the taxa used? Any advice is very appreciated, thank you!

I'm using R 4.4.2 and NetCoMi version 1.1.0.

Code used:
net <- netConstruct(data = data1,
data2 = data2,
filtSamp = "highestFreq",
dataType="count",
filtSampPar = list(highestFreq = data1_n),
taxRank = "Genus",
measure = "cclasso",
zeroMethod = "pseudoZO",
zeroPar = list(pseudocount=0.5),
sparsMethod = "threshold",
thresh = 0.3,
alpha=0.001,
adjust="adaptBH",
dissFunc = "signed",
verbose = 2,
seed = 123456)

props <- netAnalyze(net clustMethod = "cluster_fast_greedy", hubPar = "eigenvector", hubQuant = 0.95)

plot (props,
sameLayout = TRUE,
layoutGroup = "union",
featVecCol = phyla,
colorVec = colvec,
nodeColor="feature",
labelScale = FALSE,
shortenLabels = "simple", labelLength = 19,
rmSingles = "inboth",
repulsion = 0.7,
nodeSize = "clr",
cexTitle = 2,
cexNodes =8,
cexHubLabels = 0.7, cexLabels = 0.5,
nodeTransp = 0.05,
mar = c(5, 2, 5, 2.5))

[stefpeschel]

Hi!
I'm sorry, but I can't reproduce this problem and I've never seen a network like this before. I really don't know what's going on.
The number of nodes shouldn't be a problem because NetCoMi has been used to build much larger networks. Have you tried changing the graphics parameters like cexNodes, edgeWidth or some of the other parameters you use in your code?

[dheadl]

Hi,

Thanks for checking! It is odd, since it doesn't happen for all my networks but changing nodeTransp to 0 fixed this.