Plot a recurrent artificial neural network using igraph and base graphics

plot_edge_list.R

library(igraph)

# get my dataset from the structure.R file
source('structure.R')

# create graph from edgelist
# note it has to be a matrix, not a dataframe
g <- graph.edgelist(as.matrix(edge_list_values[, names(edge_list_values) %in%
                                             c("j_name", "i_name")]))
g
png('networkgraph_edgelist.png', 800, 800)
plot(g)
dev.off()

structure.R

# 14x14
# 10 hidden units on each side
# 1 bias unit connected to each of the 14 units
# 1 external unit for each of the 14 units

# head(edge_list_values)
#   weights j_name i_name
# 1   0.480   hi00   in00
# 2   0.669   hi01   in00
# 3   0.464   hi02   in00
# 4   0.727   hi03   in00
# 5   0.354   hi04   in00
# 6   0.687   hi05   in00

# > dim(edge_list_values)
# [1] 1036    3

edge_list_values <- structure(list(weights = c(0.48, 0.669, 0.464, 0.727, 0.354, 
0.687, 0.718, 0.404, 0.357, 0.711, -0.828, -0.011, 0.237, 0.561, 
0.861, 0.162, 0.528, 0.081, 0.15, 0.198, 0.235, 0.292, 0.249, 
0.392, -1, -0.028, 0.01, 0.157, 0.457, 0.16, 0.021, 0.348, -0.004, 
0.14, 0.293, -1.005, 0.2, 0.266, 0, 0.116, -0.036, 0.312, 0.053, 
-0.168, 0.074, 0.008, -0.215, -0.038, -0.038, -1, 0.187, -0.152, 
-0.06, -0.081, 0.014, 0.121, -0.097, 0.231, 0.186, -0.184, -1, 
0.243, -0.021, -0.238, -0.078, -0.134, 0.104, 0.028, 0.098, 0.027, 
0.016, -0.043, 0.096, 0.121, -1, 0.429, 0.72, 0.352, 0.525, 0.278, 
0.531, 0.625, 0.236, 0.434, 0.449, -0.971, 0.598, -0.086, 0.068, 
0.785, -0.029, 0.501, -0.001, 0.11, 0.34, 0.138, -0.019, -0.09, 
-0.037, -1, 0.66, 0.618, 0.526, 0.67, 0.544, 0.788, 0.362, 0.31, 
0.621, 0.652, -0.874, 0.561, 0.264, 0.368, 0.563, 0.116, 0.648, 
0.408, 0.176, 0.174, 0.409, 0.266, 0.398, 0.19, -1, 0.233, 0.052, 
0.033, -0.105, -0.009, 0.248, -0.138, 0.019, 0.141, -0.11, -1.018, 
0.384, 0.254, 0.257, 0.11, 0.052, -0.066, -0.06, -0.16, -0.147, 
0.046, 0.216, 0.149, 0.254, -1, 0.322, 0.681, 0.418, 0.597, 0.462, 
0.351, 0.396, 0.619, 0.554, 0.641, -0.948, 0.457, 0.325, -0.009, 
0.579, 0.793, 0.006, 0.192, 0.338, 0.264, 0.256, 0.025, 0.004, 
-0.068, -1, 0.136, 0.075, 0.115, 0.201, -0.017, 0.098, -0.06, 
-0.1, 0.157, 0.058, -1.006, 0.277, 0.253, 0.05, 0.183, -0.051, 
0.082, -0.074, 0.159, -0.094, 0.061, 0.177, 0.224, 0.108, -1, 
0.111, -0.147, 0.22, -0.158, 0.024, -0.104, 0.274, 0.082, 0.276, 
0.271, -1.007, 0.218, 0.171, -0.225, 0.047, -0.108, 0.121, 0.06, 
-0.126, -0.012, -0.094, 0.036, -0.204, 0.038, -1, 0.27, 0.213, 
0.188, 0.209, 0.141, 0.172, 0.098, 0.348, 0.479, 0.54, -1.022, 
0.482, 0.317, 0.076, 0.535, 0.472, 0.132, 0.645, 0.09, 0.015, 
0.556, 0.108, 0.028, 0.054, -1, 0.495, 0.396, 0.109, 0.379, 0.093, 
0.62, 0.062, 0.154, 0.27, 0.431, -1.025, 0.502, 0.053, 0.221, 
0.31, 0.363, 0.209, 0.259, 0.164, 0.143, 0.652, 0.038, 0.132, 
-0.05, -1, 0.094, 0.226, 0.205, 0.121, 0.222, 0.113, -0.083, 
0.001, 0.077, -0.148, -1, -0.056, 0.023, -0.249, 0.142, -0.117, 
0.027, -0.061, -0.161, 0.2, -0.03, -0.136, -0.132, 0.013, -1, 
0.047, 0.104, 0.189, -0.09, 0.006, 0.267, 0.297, 0.345, 0.312, 
0.015, -1.019, 0.065, -0.108, 0.07, 0.134, 0.412, -0.025, 0.105, 
0.095, 0.217, 0.028, 0.071, 0.1, -0.026, -1, 0.034, 0.076, 0.086, 
0.16, -0.029, 0.45, 0.096, 0.23, 0.201, 0.23, -1.03, 0.247, 0.155, 
0.002, 0.551, 0.475, -0.031, 0.429, 0.188, 0.155, 0.115, 0.08, 
0.108, 0.203, -1, 0.086, 0.261, 0.034, 0.207, 0.049, -0.058, 
0.246, 0.019, 0.293, 0.255, 0.014, -0.122, 0.074, -1.007, 0.111, 
-0.069, -0.171, 0.069, 0.155, -0.175, -0.038, 0.011, -0.09, 0.293, 
-1, 0.116, 0.286, 0.17, 0.193, 0.312, 0.343, 0.614, 0.372, 0.575, 
0.283, 0.719, 0.261, 0.683, -0.789, 0.359, 0.364, 0.311, 0.303, 
0.351, 0.661, 0.473, 0.146, 0.53, 0.329, -1, -0.075, 0.298, -0.007, 
0.145, 0.519, 0.028, 0.575, 0.695, 0.239, 0.246, 0.383, 0.6, 
0.229, -0.831, 0.391, 0.281, 0.33, 0.437, 0.546, 0.422, 0.558, 
0.414, 0.424, 0.463, -1, 0.058, 0.094, 0.421, 0.197, 0.416, 0.239, 
0.31, 0.509, 0.203, 0.324, 0.425, 0.132, 0.328, -1.023, 0.081, 
0.502, 0.473, 0.031, 0.279, 0.305, 0.197, 0.445, 0.297, 0.344, 
-1, -0.034, 0.221, 0.093, 0.229, 0.082, 0.281, 0.073, -0.008, 
0.035, 0.335, 0.172, 0.024, 0.234, -1.016, 0.093, 0.175, 0.027, 
0.098, 0.287, -0.077, 0.102, 0.346, 0.149, -0.065, -1, -0.007, 
0.551, 0.615, 0.27, 0.236, 0.231, 0.609, 0.316, 0.325, 0.273, 
0.542, 0.635, 0.346, -0.826, 0.344, 0.434, 0.303, 0.473, 0.278, 
0.35, 0.489, 0.258, 0.31, 0.525, -1, -0.067, 0.159, 0.181, 0.32, 
0.036, 0.293, 0.525, 0.155, 0.124, 0.376, 0.179, 0.205, 0.587, 
-1.026, 0.465, 0.192, 0.433, 0.299, 0.305, 0.07, 0.209, 0.472, 
0.276, 0.452, -1, 0.213, 0.442, 0.514, 0.411, 0.313, 0.439, 0.368, 
0.51, 0.125, 0.456, 0.298, 0.331, 0.287, -0.799, 0.637, 0.633, 
0.527, 0.295, 0.193, 0.28, 0.282, 0.536, 0.718, 0.414, -1, 0.357, 
0.618, 0.5, 0.312, 0.004, 0.267, 0.125, 0.254, 0.464, 0.206, 
0.421, 0.536, 0.379, -0.835, 0.242, 0.537, 0.263, 0.646, 0.518, 
0.22, 0.312, 0.564, 0.692, 0.532, -1, 0.236, 0.217, 0.353, 0.44, 
0.243, 0.62, 0.352, 0.334, 0.331, 0.301, 0.396, 0.584, 0.248, 
-0.906, 0.231, 0.384, 0.317, 0.407, 0.154, 0.679, 0.348, 0.442, 
0.512, 0.453, -1, -0.011, 0.57, 0.26, 0.175, -0.088, 0.405, 0.027, 
0.522, 0.413, 0.21, 0.399, 0.457, 0.38, -0.93, 0.399, 0.301, 
0.35, 0.574, 0.436, 0.297, 0.269, 0.381, 0.191, 0.498, -1, 0.19, 
0.483, 0.612, 0.259, 0.032, 0.449, 0.093, 0.404, 0.321, 0.456, 
0.279, 0.246, 0.272, -0.825, 0.591, 0.321, 0.487, 0.303, 0.106, 
0.565, 0.32, 0.465, 0.682, 0.225, -1, 0.098, 0.575, 0.466, 0.339, 
0.149, 0.537, 0.202, 0.403, 0.406, 0.196, 0.249, 0.708, 0.44, 
-0.818, 0.309, 0.263, 0.459, 0.251, 0.552, 0.254, 0.519, 0.279, 
0.655, 0.105, -1, 0.234, 0.407, 0.524, 0.119, 0.145, 0.506, 0.425, 
0.544, 0.261, 0.172, 0.535, 0.386, 0.364, -0.855, 0.405, 0.502, 
0.289, 0.205, 0.168, 0.624, 0.194, 0.196, 0.491, 0.228, -1, 0.3, 
-0.209, -0.082, -0.052, -0.002, 0.191, 0.136, 0.162, 0.272, -0.13, 
-0.153, -0.053, -0.114, -0.143, 0.27, 0.057, 0.077, -0.08, -0.053, 
0.007, 0.233, 0.238, -0.02, 0.181, -0.16, 0.163, -0.174, 0.12, 
-0.096, -0.094, -0.209, 0.253, 0.17, 0.009, 0.1, -0.028, 0.026, 
0.079, 0.095, -0.001, -0.155, 0.166, -0.106, 0.027, -0.035, 0.054, 
0.194, 0.122, -0.048, -0.087, -0.093, 0.053, 0.139, 0.142, 0.147, 
0.275, 0.098, -0.048, -0.143, -0.22, -0.151, -0.231, 0.001, -0.199, 
0.208, -0.05, -0.222, 0.262, 0.046, 0.111, 0.194, -0.062, 0.125, 
0.039, 0.322, -0.185, 0.143, 0.046, 0.211, 0.056, 0.255, -0.178, 
0.069, 0.289, -0.038, 0.005, -0.101, -0.029, -0.059, 0.132, -0.113, 
0.153, -0.193, -0.012, 0.174, 0.168, -0.041, -0.198, 0.196, -0.179, 
0.169, 0.2, -0.034, 0.091, 0.056, -0.086, 0.134, -0.085, -0.05, 
-0.117, -0.067, 0.254, -0.12, -0.169, -0.018, 0.141, 0.027, -0.04, 
-0.149, 0.086, -0.079, 0.279, -0.145, 0.078, 0.024, 0.185, 0.206, 
-0.028, -0.067, 0.174, 0.208, 0.1, 0.176, 0.243, 0.212, 0.261, 
0.266, 0.081, 0.122, 0.234, -0.097, 0.287, -0.154, -0.211, 0.112, 
0.182, -0.082, 0.027, 0.18, 0.272, -0.1, -0.153, 0.274, 0.049, 
0.146, -0.051, 0.294, 0.163, 0.089, -0.052, 0.213, -0.148, 0.002, 
-0.128, 0.011, 0.029, 0.248, 0.231, 0.244, 0.241, 0.064, 0.21, 
-0.032, -0.073, 0.087, -0.117, -0.047, -0.12, -0.04, 0.253, 0.15, 
0.214, -0.184, 0.251, -0.103, 0.25, -0.049, -0.163, -0.001, -0.174, 
-0.18, 0.212, 0.045, 0.06, 0.021, 0.289, -0.161, -0.027, 0.137, 
-0.18, -0.198, -0.039, 0.118, -0.077, -0.138, -0.195, -0.013, 
-0.025, 0.125, -0.047, -0.084, 0.262, 0.215, 0.035, 0.124, 0.022, 
-0.132, 0.121, -0.137, 0.24, 0.264, 0.292, -0.057, 0.202, 0.194, 
-0.171, 0.21, 0.224, -0.083, 0.282, 0.154, 0.155, -0.077, 0.251, 
-0.007, -0.118, 0.077, -0.135, -0.043, -0.084, -0.059, 0.3, 0.076, 
-0.05, -0.116, -0.044, 0.022, -0.079, -0.165, 0.085, 0.083, 0.164, 
0.141, 0.174, 0.128, 0.121, -0.073, 0.283, -0.038, 0.122, 0.282, 
0.287, 0.257, 0.258, 0.276, 0.199, -0.132, -0.157, 0.277, 0.138, 
0.067, -0.039, -0.125, 0.136, -0.117, -0.166, 0.111, 0.163, -0.079, 
0.222, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), j_name = c("hi00", 
"hi01", "hi02", "hi03", "hi04", "hi05", "hi06", "hi07", "hi08", 
"hi09", "im00", "in01", "in02", "in03", "in04", "in05", "in06", 
"in07", "in08", "in09", "in10", "in11", "in12", "in13", "im00", 
"hi00", "hi01", "hi02", "hi03", "hi04", "hi05", "hi06", "hi07", 
"hi08", "hi09", "im01", "in00", "in02", "in03", "in04", "in05", 
"in06", "in07", "in08", "in09", "in10", "in11", "in12", "in13", 
"im01", "hi00", "hi01", "hi02", "hi03", "hi04", "hi05", "hi06", 
"hi07", "hi08", "hi09", "im02", "in00", "in01", "in03", "in04", 
"in05", "in06", "in07", "in08", "in09", "in10", "in11", "in12", 
"in13", "im02", "hi00", "hi01", "hi02", "hi03", "hi04", "hi05", 
"hi06", "hi07", "hi08", "hi09", "im03", "in00", "in01", "in02", 
"in04", "in05", "in06", "in07", "in08", "in09", "in10", "in11", 
"in12", "in13", "im03", "hi00", "hi01", "hi02", "hi03", "hi04", 
"hi05", "hi06", "hi07", "hi08", "hi09", "im04", "in00", "in01", 
"in02", "in03", "in05", "in06", "in07", "in08", "in09", "in10", 
"in11", "in12", "in13", "im04", "hi00", "hi01", "hi02", "hi03", 
"hi04", "hi05", "hi06", "hi07", "hi08", "hi09", "im05", "in00", 
"in01", "in02", "in03", "in04", "in06", "in07", "in08", "in09", 
"in10", "in11", "in12", "in13", "im05", "hi00", "hi01", "hi02", 
"hi03", "hi04", "hi05", "hi06", "hi07", "hi08", "hi09", "im06", 
"in00", "in01", "in02", "in03", "in04", "in05", "in07", "in08", 
"in09", "in10", "in11", "in12", "in13", "im06", "hi00", "hi01", 
"hi02", "hi03", "hi04", "hi05", "hi06", "hi07", "hi08", "hi09", 
"im07", "in00", "in01", "in02", "in03", "in04", "in05", "in06", 
"in08", "in09", "in10", "in11", "in12", "in13", "im07", "hi00", 
"hi01", "hi02", "hi03", "hi04", "hi05", "hi06", "hi07", "hi08", 
"hi09", "im08", "in00", "in01", "in02", "in03", "in04", "in05", 
"in06", "in07", "in09", "in10", "in11", "in12", "in13", "im08", 
"hi00", "hi01", "hi02", "hi03", "hi04", "hi05", "hi06", "hi07", 
"hi08", "hi09", "im09", "in00", "in01", "in02", "in03", "in04", 
"in05", "in06", "in07", "in08", "in10", "in11", "in12", "in13", 
"im09", "hi00", "hi01", "hi02", "hi03", "hi04", "hi05", "hi06", 
"hi07", "hi08", "hi09", "im10", "in00", "in01", "in02", "in03", 
"in04", "in05", "in06", "in07", "in08", "in09", "in11", "in12", 
"in13", "im10", "hi00", "hi01", "hi02", "hi03", "hi04", "hi05", 
"hi06", "hi07", "hi08", "hi09", "im11", "in00", "in01", "in02", 
"in03", "in04", "in05", "in06", "in07", "in08", "in09", "in10", 
"in12", "in13", "im11", "hi00", "hi01", "hi02", "hi03", "hi04", 
"hi05", "hi06", "hi07", "hi08", "hi09", "im12", "in00", "in01", 
"in02", "in03", "in04", "in05", "in06", "in07", "in08", "in09", 
"in10", "in11", "in13", "im12", "hi00", "hi01", "hi02", "hi03", 
"hi04", "hi05", "hi06", "hi07", "hi08", "hi09", "im13", "in00", 
"in01", "in02", "in03", "in04", "in05", "in06", "in07", "in08", 
"in09", "in10", "in11", "in12", "im13", "im01", "im02", "im03", 
"im04", "im05", "im06", "im07", "im08", "im09", "im10", "im11", 
"im12", "im13", "in00", "hm00", "hm01", "hm02", "hm03", "hm04", 
"hm05", "hm06", "hm07", "hm08", "hm09", "in00", "im00", "im02", 
"im03", "im04", "im05", "im06", "im07", "im08", "im09", "im10", 
"im11", "im12", "im13", "in01", "hm00", "hm01", "hm02", "hm03", 
"hm04", "hm05", "hm06", "hm07", "hm08", "hm09", "in01", "im00", 
"im01", "im03", "im04", "im05", "im06", "im07", "im08", "im09", 
"im10", "im11", "im12", "im13", "in02", "hm00", "hm01", "hm02", 
"hm03", "hm04", "hm05", "hm06", "hm07", "hm08", "hm09", "in02", 
"im00", "im01", "im02", "im04", "im05", "im06", "im07", "im08", 
"im09", "im10", "im11", "im12", "im13", "in03", "hm00", "hm01", 
"hm02", "hm03", "hm04", "hm05", "hm06", "hm07", "hm08", "hm09", 
"in03", "im00", "im01", "im02", "im03", "im05", "im06", "im07", 
"im08", "im09", "im10", "im11", "im12", "im13", "in04", "hm00", 
"hm01", "hm02", "hm03", "hm04", "hm05", "hm06", "hm07", "hm08", 
"hm09", "in04", "im00", "im01", "im02", "im03", "im04", "im06", 
"im07", "im08", "im09", "im10", "im11", "im12", "im13", "in05", 
"hm00", "hm01", "hm02", "hm03", "hm04", "hm05", "hm06", "hm07", 
"hm08", "hm09", "in05", "im00", "im01", "im02", "im03", "im04", 
"im05", "im07", "im08", "im09", "im10", "im11", "im12", "im13", 
"in06", "hm00", "hm01", "hm02", "hm03", "hm04", "hm05", "hm06", 
"hm07", "hm08", "hm09", "in06", "im00", "im01", "im02", "im03", 
"im04", "im05", "im06", "im08", "im09", "im10", "im11", "im12", 
"im13", "in07", "hm00", "hm01", "hm02", "hm03", "hm04", "hm05", 
"hm06", "hm07", "hm08", "hm09", "in07", "im00", "im01", "im02", 
"im03", "im04", "im05", "im06", "im07", "im09", "im10", "im11", 
"im12", "im13", "in08", "hm00", "hm01", "hm02", "hm03", "hm04", 
"hm05", "hm06", "hm07", "hm08", "hm09", "in08", "im00", "im01", 
"im02", "im03", "im04", "im05", "im06", "im07", "im08", "im10", 
"im11", "im12", "im13", "in09", "hm00", "hm01", "hm02", "hm03", 
"hm04", "hm05", "hm06", "hm07", "hm08", "hm09", "in09", "im00", 
"im01", "im02", "im03", "im04", "im05", "im06", "im07", "im08", 
"im09", "im11", "im12", "im13", "in10", "hm00", "hm01", "hm02", 
"hm03", "hm04", "hm05", "hm06", "hm07", "hm08", "hm09", "in10", 
"im00", "im01", "im02", "im03", "im04", "im05", "im06", "im07", 
"im08", "im09", "im10", "im12", "im13", "in11", "hm00", "hm01", 
"hm02", "hm03", "hm04", "hm05", "hm06", "hm07", "hm08", "hm09", 
"in11", "im00", "im01", "im02", "im03", "im04", "im05", "im06", 
"im07", "im08", "im09", "im10", "im11", "im13", "in12", "hm00", 
"hm01", "hm02", "hm03", "hm04", "hm05", "hm06", "hm07", "hm08", 
"hm09", "in12", "im00", "im01", "im02", "im03", "im04", "im05", 
"im06", "im07", "im08", "im09", "im10", "im11", "im12", "in13", 
"hm00", "hm01", "hm02", "hm03", "hm04", "hm05", "hm06", "hm07", 
"hm08", "hm09", "in13", "in00", "in01", "in02", "in03", "in04", 
"in05", "in06", "in07", "in08", "in09", "in10", "in11", "in12", 
"in13", "in00", "in01", "in02", "in03", "in04", "in05", "in06", 
"in07", "in08", "in09", "in10", "in11", "in12", "in13", "in00", 
"in01", "in02", "in03", "in04", "in05", "in06", "in07", "in08", 
"in09", "in10", "in11", "in12", "in13", "in00", "in01", "in02", 
"in03", "in04", "in05", "in06", "in07", "in08", "in09", "in10", 
"in11", "in12", "in13", "in00", "in01", "in02", "in03", "in04", 
"in05", "in06", "in07", "in08", "in09", "in10", "in11", "in12", 
"in13", "in00", "in01", "in02", "in03", "in04", "in05", "in06", 
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