How to create a graph from an adjacency matrix?

Usage
1

Hello, everyone.

I am trying to create a network graph using the igraph package.

Briefly, I have an adjacency matrix where each node is a species (total of 23 species) and the links are the values of the Müller Index.

I can run the script normally, but instead of having 23 nodes, only 7 appear, and those 7 do not correspond to the species, but to the index values. Does anyone know how to solve this problem?

Here is my script:

library (igraph)

data = read.table ("Data_Muller2.txt", dec = ",")

View (data)

class (data) # the object's class is data frame, that's why in the next line I put graph_from_data_frame #

network <- graph_from_data_frame (data)

plot (network, edge.arrow.size = 0.2, layout = layout_with_graphopt)

grafo
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Thank you,

Caroline

2

If you have an adjacency matrix, use graph_from_adjacency_matrix. Check the documentation for the requirement on the input data format.

The documentation (see graph_from_data_frame) explains how dataframes are converted to graphs, and it is clear that they are not interpreted as adjacency matrices.

Convert your input to a matrix.

3

Dear, szhorvat.
Thank you for your contribution. The problem was exactly the one you pointed out.

4

Dear,
My problem now is another.
The nodes appear the way I want, but the edges connecting the nodes do not appear.
When I evaluate my network, the following appears:

IGRAPH e901f03 DN-- 23 0 -

  • attr: name (v / c)
  • edges from e901f03 (vertex names):

This is my new script:

library (igraph)

data = structure(list(Adenocalymma_adenophorum = c(NA, 0, 0, 0, 0.003122927, 
0.00999241, 0.008685473, 0.007730365, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0.003573423, 0, 0, 0, 0, 0), Adenocalymma_cf_bracteosum = c(0L, 
NA, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L), Adenocalymma_flaviflorum = c(0L, 0L, 
NA, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L), Adenocalymma_japurensis = c(0L, 0L, 0L, 
NA, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L), Adenocalymma_longilinium = c(0.18893711, 0, 
0, 0, NA, 0.183237263, 0.139293056, 0.120902907, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0.132071652, 0, 0.457142857, 0.114500717
), Adenocalymma_moringifolium = c(0.322255215, 0, 0, 0, 0.097676062, 
NA, 0.261095249, 0.131416203, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.146191646, 
0, 0, 0, 0), Adenocalymma_neoflavidum = c(0.086854728, 0, 0, 
0, 0.023023646, 0.080959767, NA, 0.034786642, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Adenocalymma_tanaeciicarpum = c(0.09469697, 
0, 0, 0, 0.024480341, 0.049917782, 0.042613636, NA, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0.255554962, 0, 0, 0, 0), Amphilophium_parkeri = c(0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L), Anemopaegma_robustum = c(0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L), Bignonia_aequinoctialis = c(0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L), Bignonia_prieurei = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, NA, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L
), Calichlamys_latifolia = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, NA, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), 
    Fridericia_cf_trailli = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.765625, 
    0, 0, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0), Fridericia_chica = c(0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L), Fridericia_cinamomea = c(0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L), Fridericia_nigrescens = c(0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
    NA, 0L, 0L, 0L, 0L, 0L, 0L), Fridericia_prancei = c(0.040201005, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, 0, 0, 
    0, 0, 0), Fridericia_triplinervia = c(0, 0, 0, 0, 0, 0.041930937, 
    0, 0.192970073, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, 0, 0, 0, 
    0), Pachyptera_aromatica = c(0, 0, 0, 0, 0.030562035, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, 0, 0, 0), Pleonotoma_albiflora = c(0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, NA, 0L, 0L), Pleonotoma_melioides = c(0, 
    0, 0, 0, 0.151121606, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, NA, 0.039751553), Tynanthus_panurensis = c(0, 
    0, 0, 0, 0, 0.026693325, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0.011428571, NA)), class = "data.frame", row.names = c("Adenocalymma_adenophorum", 
"Adenocalymma_cf_bracteosum", "Adenocalymma_flaviflorum", "Adenocalymma_japurensis", 
"Adenocalymma_longilinium", "Adenocalymma_moringifolium", "Adenocalymma_neoflavidum", 
"Adenocalymma_tanaeciicarpum", "Amphilophium_parkeri", "Anemopaegma_robustum", 
"Bignonia_aequinoctialis", "Bignonia_prieurei", "Calichlamys_latifolia", 
"Fridericia_cf_trailli", "Fridericia_chica", "Fridericia_cinamomea", 
"Fridericia_nigrescens", "Fridericia_prancei", "Fridericia_triplinervia", 
"Pachyptera_aromatica", "Pleonotoma_albiflora", "Pleonotoma_melioides", 
"Tynanthus_panurensis"))

View (data)

class (data)

data = data.matrix (data, rownames.force = NA) #
class (data)

network <- graph_from_adjacency_matrix (data)

plot (network, edge.arrow.size = .5, vertex.color = "gold", vertex.size = 15,
vertex.frame.color = "gray", vertex.label.color = "black",
vertex.label.cex = 0.8, vertex.label.dist = 2, edge.curved = 0.2)

Can you tell what is causing this absence of edges?

Thank you.

new
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