How to Control the Igraph Plot Layout with Fixed Positions

igraph fixed node coordinates layout

The answer to your first question is in the source code of the plot.igraph function; type plot.igraph in the R prompt to get the full source code. There is a part in there which says:

layout <- layout.norm(layout, -1, 1, -1, 1)

layout.norm is another function of igraph which does the magic for you; type layout.norm to see how it works.

Now, the answer to the second question is really simple; just pass rescale=F to the arguments of plot, which makes igraph skip the entire branch in plot.igraph where layout.norm is called, so it will work with your original coordinates. You can then use xlim and ylim as usual to set the limits of the X and Y axes.

How to plot the igraph subgraphs with saving the nodes' positions and ids?

Try the code below

library(igraph)
set.seed(1)
n <- 10
A <- matrix(sample(0:1, n * n, rep = TRUE), n, n)
diag(A) <- 0
g <- graph_from_adjacency_matrix(A)

id1 <- sort(as.integer(sample(V(g), size = n %/% 2, replace = FALSE)))
id2 <- sort(as.integer(sample(V(g), size = n %/% 2, replace = FALSE)))

g1 <- induced_subgraph(g, vids = id1)
g2 <- induced_subgraph(g, vids = id2)

par(mfrow = c(1,3))

layout <- layout.fruchterman.reingold(g)

layout2 <- layout[id2, ]

plot(g, layout = layout, main = "G")
plot(g1, layout = layout[id1, ], main = "G1")
plot(g2, layout = layout[id2, ], main = "G2")

How to pass a fixed igraph layout to plot.networx in phangorn?

plot.networx calls phangorn:::coords to get the coords which (for 2D) creates an igraph object and then uses layout.kamada.kawai. This is all hard-coded into plot.networx so not flexible enough such that you could use another layout algorithm.

You could follow the code in phangorn:::coords to create the graph layout and replace the layout function with another one, and then call phangorn:::plot2D with those coords. See plot.networx to see how to call phangorn:::plot2D correctly.

How to set fix node positions with ggnet2

Ok, this is an old question but in case anyone looks for the answer...

Make a matrix of the coordinates:

l = as.matrix(data.frame(x = c(0.1,0.1, 0.5, 0.8), y = c(0.75, 0.25, 0.5, 0.5)))

Use

ggnet2(net, mode = l)

Setting the order of circle layout to decreasing changes the nodes position in the igraph network

You could get the vertices number sequence and inverse it :

vertices <- as.numeric(V(gph2))
inverse_order <- vertices[length(vertices):1]
plot(gph2, layout = rot(layout_in_circle(gph2, order = inverse_order)))

How to create plots in iGraph in R with matching node coordinates (and removing nodes with no edges)

I would compute the coordinates on g_overall and then make the plots on the subgraphs with the coordinates previously calculated (once the coordinates of the nodes that are no longer in the graphs are removed). In other words:

set.seed(123)

g_overall = erdos.renyi.game(25, 0.3)

coords = layout_as_tree(g_overall,
                    root = 1,
                    circular = FALSE,
                    flip.y = FALSE,
                    mode = "all")

removals1 = c("2" ,"5" ,"13", "19", "25")
removals2 = c("2" ,"5" ,"11", "13", "19", "22", "24", "25")

g1 = delete_vertices(g_overall, removals1)
g2 = delete_vertices(g_overall, removals2)

plot.igraph(g1,
        layout = coords[-as.numeric(removals),])

plot.igraph(g2,
        layout = coords[-as.numeric(removals),])

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