How to plot one-mode unipartite network in R from a bipartite matrix

I have a matrix in which the columns are predators and the rows are the prey they eat. I want to plot an one-mode network of the predators. So, each node it will be the predators and the link/edges will connect the predators that share prey.

My original dataset has much more zero that the example below, but I got close to what I want to plot with the code below:

m <- matrix(ncol=40,nrow=20)
m <- apply(m, c(1,2), function(x) sample(c(0:4),1)) 
colnames (m) <- c(sprintf("C%02d", seq(1,40)))
rownames (m) <- c(sprintf("R%02d", seq(1,20)))


install.packages("GGally")
library(GGally)

ggnet2(as.one.mode(m, project="higher"), label=T,
       node.size = 2, node.color = "black",
       edge.size = 0.1, edge.color = "grey",
       layout.par = list(cell.jitter = 3))

The nodes on my plot are overlapping a lot (as in the image, that is from my original dataset).

Any ideas on how to change the nodes overlapping? I tried to change layout parameters already.

Also, I couldn't plot this one-mode/unipartite network using igraph. Any ideas on how to plot this type of network from a bipartite matrix with igraph?

Any sugestions on how to improve the visualization of this type of network is welcome, including using other packages and functions

Solution

The code you provide generates a fairly dense graph, so it will be tricky to find a layout without overlapping in this case. You could look into some options other than "ball and stick" layouts, and see if those work for you.

I find the combination of tidygraph and ggraph very powerful and intuitive for working with networks. A quick demo of projecting and plotting a bipartite graph:

library(tidygraph)
library(ggraph)

m <- matrix(ncol=40,nrow=20)
m <- apply(m, c(1,2), function(x) sample(c(0:4),1)) 
colnames (m) <- c(sprintf("C%02d", seq(1,40)))
rownames (m) <- c(sprintf("R%02d", seq(1,20)))

tg <- as_tbl_graph(m)

tg_proj <- igraph::bipartite_projection(tg, which=TRUE) |> 
    as_tbl_graph()

midw <- tg_proj %E>% pull(weight) |> median()

ggraph(tg_proj, layout="kk") +
    geom_edge_link(aes(col=weight), alpha=0.5, edge_width=1.2) +
    geom_node_point() +
    scale_edge_color_gradient2(midpoint=midw) +
    theme(plot.background=element_rect(color="gray40"))