Plot network with size node based on their degree

Question

I create a network and then I would like to plot network nodes size based on degree (more links -> larger node). I try the code thati I found here .

That's my code:

library(igraph)

# load dataset
net <- read.graph("./dataset.gml", format = c("gml"))

# Generate colors base on media type:
colrs <- c("gray50", "tomato", "gold")
V(net)$color <- colrs[V(net)$media.type]

# Compute node degrees (#links) and use that to set node size:
deg <- degree(net, mode = "all")
V(net)$size <- deg*3
# We could also use the audience size value:
V(net)$size <- V(net)$audience.size*0.6

#change arrow size and edge color:
E(net)$arrow.size <- .2
E(net)$edge.color <- "gray80"

x11()
plot(net)

When I run this code I get this error:

deg <- degree(net, mode = "all")

Error in degree(net, mode = "all") : unused argument (mode = "all")

---

The dataset I used is Les Miserables:

> dput(net)
structure(list(77, FALSE, c(1, 2, 3, 3, 4, 5, 6, 7, 8, 9, 11, 
11, 11, 11, 12, 13, 14, 15, 17, 18, 18, 19, 19, 19, 20, 20, 20, 
20, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 
23, 23, 23, 23, 23, 24, 24, 25, 25, 25, 26, 26, 26, 26, 27, 27, 
27, 27, 27, 28, 28, 29, 29, 29, 30, 31, 31, 31, 31, 32, 33, 33, 
34, 34, 35, 35, 35, 36, 36, 36, 36, 37, 37, 37, 37, 37, 38, 38, 
38, 38, 38, 38, 39, 40, 41, 41, 42, 42, 42, 43, 43, 43, 44, 44, 
45, 47, 48, 48, 48, 48, 49, 49, 50, 50, 51, 51, 51, 52, 52, 53, 
54, 54, 54, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 56, 56, 57, 
57, 57, 58, 58, 58, 58, 58, 59, 59, 59, 59, 60, 60, 60, 61, 61, 
61, 61, 61, 61, 62, 62, 62, 62, 62, 62, 62, 62, 63, 63, 63, 63, 
63, 63, 63, 63, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 65, 65, 
65, 65, 65, 65, 65, 65, 65, 65, 66, 66, 66, 66, 66, 66, 66, 66, 
66, 67, 68, 68, 68, 68, 68, 68, 69, 69, 69, 69, 69, 69, 69, 70, 
70, 70, 70, 70, 70, 70, 70, 71, 71, 71, 71, 71, 71, 71, 71, 72, 
72, 72, 73, 74, 74, 75, 75, 75, 75, 75, 75, 75, 76, 76, 76, 76, 
76, 76, 76), c(0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 10, 3, 2, 0, 11, 
11, 11, 11, 16, 16, 17, 16, 17, 18, 16, 17, 18, 19, 16, 17, 18, 
19, 20, 16, 17, 18, 19, 20, 21, 16, 17, 18, 19, 20, 21, 22, 12, 
11, 23, 11, 24, 23, 11, 24, 11, 16, 25, 11, 23, 25, 24, 26, 11, 
27, 23, 27, 11, 23, 30, 11, 23, 27, 11, 11, 27, 11, 29, 11, 34, 
29, 34, 35, 11, 29, 34, 35, 36, 11, 29, 34, 35, 36, 37, 11, 29, 
25, 25, 24, 25, 41, 25, 24, 11, 26, 27, 28, 11, 28, 46, 47, 25, 
27, 11, 26, 11, 49, 24, 49, 26, 11, 51, 39, 51, 51, 49, 26, 51, 
49, 39, 54, 26, 11, 16, 25, 41, 48, 49, 55, 55, 41, 48, 55, 48, 
27, 57, 11, 58, 55, 48, 57, 48, 58, 59, 48, 58, 60, 59, 57, 55, 
55, 58, 59, 48, 57, 41, 61, 60, 59, 48, 62, 57, 58, 61, 60, 55, 
55, 62, 48, 63, 58, 61, 60, 59, 57, 11, 63, 64, 48, 62, 58, 61, 
60, 59, 57, 55, 64, 58, 59, 62, 65, 48, 63, 61, 60, 57, 25, 11, 
24, 27, 48, 41, 25, 68, 11, 24, 27, 48, 41, 25, 69, 68, 11, 24, 
27, 41, 58, 27, 69, 68, 70, 11, 48, 41, 25, 26, 27, 11, 48, 48, 
73, 69, 68, 25, 48, 41, 70, 71, 64, 65, 66, 63, 62, 48, 58), 
    c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 12, 11, 10, 14, 15, 16, 
    17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 
    32, 33, 34, 35, 36, 37, 38, 47, 46, 39, 40, 41, 42, 43, 44, 
    45, 49, 48, 52, 51, 50, 54, 55, 53, 56, 57, 58, 60, 59, 61, 
    62, 63, 66, 64, 65, 67, 69, 70, 71, 68, 72, 73, 74, 75, 76, 
    77, 79, 78, 82, 83, 80, 81, 87, 88, 84, 85, 86, 93, 94, 89, 
    90, 91, 92, 95, 96, 97, 98, 101, 100, 99, 102, 103, 104, 
    106, 105, 107, 108, 112, 110, 111, 109, 114, 113, 116, 115, 
    119, 118, 117, 121, 120, 122, 125, 124, 123, 131, 132, 133, 
    130, 128, 134, 135, 127, 126, 129, 136, 137, 139, 140, 138, 
    145, 143, 142, 141, 144, 148, 147, 149, 146, 150, 151, 152, 
    153, 158, 157, 154, 156, 155, 164, 162, 159, 163, 160, 161, 
    166, 165, 168, 174, 170, 171, 167, 173, 172, 169, 184, 177, 
    175, 183, 179, 182, 181, 180, 176, 178, 187, 194, 193, 189, 
    192, 191, 190, 188, 185, 186, 200, 196, 197, 203, 202, 198, 
    201, 195, 199, 204, 206, 207, 205, 208, 210, 209, 213, 214, 
    211, 215, 217, 216, 212, 221, 222, 218, 223, 224, 225, 220, 
    219, 230, 233, 226, 232, 231, 228, 227, 229, 236, 234, 235, 
    237, 238, 239, 242, 244, 243, 241, 240, 245, 246, 252, 253, 
    251, 250, 247, 248, 249), c(0, 1, 2, 4, 5, 6, 7, 8, 9, 13, 
    3, 12, 11, 10, 14, 15, 16, 17, 47, 49, 52, 54, 57, 62, 66, 
    69, 72, 73, 75, 77, 82, 87, 93, 102, 106, 112, 114, 119, 
    131, 145, 184, 206, 213, 221, 230, 236, 46, 18, 19, 21, 24, 
    28, 33, 39, 55, 132, 20, 22, 25, 29, 34, 40, 23, 26, 30, 
    35, 41, 27, 31, 36, 42, 32, 37, 43, 38, 44, 45, 48, 51, 58, 
    64, 67, 70, 50, 53, 60, 97, 101, 116, 207, 214, 222, 56, 
    59, 95, 96, 98, 100, 110, 133, 205, 211, 218, 233, 242, 61, 
    103, 113, 118, 125, 130, 234, 63, 65, 71, 74, 104, 111, 143, 
    208, 215, 223, 226, 235, 105, 107, 76, 79, 83, 88, 94, 68, 
    78, 80, 84, 89, 81, 85, 90, 86, 91, 92, 121, 128, 99, 134, 
    139, 164, 210, 217, 224, 232, 244, 108, 109, 135, 140, 142, 
    148, 150, 153, 162, 168, 177, 187, 200, 209, 216, 231, 237, 
    238, 243, 252, 115, 117, 124, 127, 136, 120, 122, 123, 126, 
    129, 137, 138, 141, 147, 158, 159, 174, 175, 194, 144, 149, 
    157, 163, 170, 183, 193, 204, 146, 151, 154, 160, 171, 179, 
    189, 196, 225, 253, 152, 156, 161, 167, 182, 192, 197, 155, 
    166, 173, 181, 191, 203, 165, 172, 180, 190, 202, 169, 176, 
    188, 198, 251, 178, 185, 201, 250, 186, 195, 247, 199, 248, 
    249, 212, 220, 228, 241, 219, 227, 240, 229, 245, 246, 239
    ), c(0, 0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 10, 14, 15, 16, 17, 
    18, 18, 19, 21, 24, 28, 33, 39, 48, 50, 53, 57, 62, 64, 67, 
    68, 72, 73, 75, 77, 80, 84, 89, 95, 96, 97, 99, 102, 105, 
    107, 108, 108, 109, 113, 115, 117, 120, 122, 123, 126, 136, 
    138, 141, 146, 150, 153, 159, 167, 175, 185, 195, 204, 205, 
    211, 218, 226, 234, 237, 238, 240, 247, 254), c(0, 10, 10, 
    12, 13, 13, 13, 13, 13, 13, 13, 14, 46, 47, 47, 47, 47, 56, 
    62, 67, 71, 74, 76, 77, 83, 92, 105, 112, 124, 126, 131, 
    132, 132, 132, 132, 136, 139, 141, 142, 142, 144, 144, 153, 
    153, 153, 153, 153, 154, 155, 173, 178, 178, 182, 182, 182, 
    183, 192, 192, 200, 210, 217, 223, 228, 233, 237, 240, 242, 
    243, 243, 247, 250, 252, 253, 253, 254, 254, 254, 254), list(
        c(1, 0, 1), structure(list(), .Names = character(0)), 
        structure(list(id = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 
        11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 
        25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 
        39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 
        53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 
        67, 68, 69, 70, 71, 72, 73, 74, 75, 76), label = c("Myriel", 
        "Napoleon", "MlleBaptistine", "MmeMagloire", "CountessDeLo", 
        "Geborand", "Champtercier", "Cravatte", "Count", "OldMan", 
        "Labarre", "Valjean", "Marguerite", "MmeDeR", "Isabeau", 
        "Gervais", "Tholomyes", "Listolier", "Fameuil", "Blacheville", 
        "Favourite", "Dahlia", "Zephine", "Fantine", "MmeThenardier", 
        "Thenardier", "Cosette", "Javert", "Fauchelevent", "Bamatabois", 
        "Perpetue", "Simplice", "Scaufflaire", "Woman1", "Judge", 
        "Champmathieu", "Brevet", "Chenildieu", "Cochepaille", 
        "Pontmercy", "Boulatruelle", "Eponine", "Anzelma", "Woman2", 
        "MotherInnocent", "Gribier", "Jondrette", "MmeBurgon", 
        "Gavroche", "Gillenormand", "Magnon", "MlleGillenormand", 
        "MmePontmercy", "MlleVaubois", "LtGillenormand", "Marius", 
        "BaronessT", "Mabeuf", "Enjolras", "Combeferre", "Prouvaire", 
        "Feuilly", "Courfeyrac", "Bahorel", "Bossuet", "Joly", 
        "Grantaire", "MotherPlutarch", "Gueulemer", "Babet", 
        "Claquesous", "Montparnasse", "Toussaint", "Child1", 
        "Child2", "Brujon", "MmeHucheloup"), maincharacter = c(0, 
        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 
        0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
        1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
        0, 0, 0, 0)), .Names = c("id", "label", "maincharacter"
        )), structure(list(value = c(1, 8, 10, 6, 1, 1, 1, 1, 
        2, 1, 1, 3, 3, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 3, 3, 
        3, 4, 3, 3, 3, 3, 5, 3, 3, 3, 3, 4, 4, 3, 3, 3, 3, 4, 
        4, 4, 2, 9, 2, 7, 13, 1, 12, 4, 31, 1, 1, 17, 5, 5, 1, 
        1, 8, 1, 1, 1, 2, 1, 2, 3, 2, 1, 1, 2, 1, 3, 2, 3, 3, 
        2, 2, 2, 2, 1, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 1, 1, 1, 
        2, 3, 2, 2, 1, 3, 1, 1, 3, 1, 2, 1, 2, 1, 1, 1, 3, 2, 
        1, 1, 9, 2, 2, 1, 1, 1, 2, 1, 1, 6, 12, 1, 1, 21, 19, 
        1, 2, 5, 4, 1, 1, 1, 1, 1, 7, 7, 6, 1, 4, 15, 5, 6, 2, 
        1, 4, 2, 2, 6, 2, 5, 1, 1, 9, 17, 13, 7, 2, 1, 6, 3, 
        5, 5, 6, 2, 4, 3, 2, 1, 5, 12, 5, 4, 10, 6, 2, 9, 1, 
        1, 5, 7, 3, 5, 5, 5, 2, 5, 1, 2, 3, 3, 1, 2, 2, 1, 1, 
        1, 1, 3, 5, 1, 1, 1, 1, 1, 6, 6, 1, 1, 2, 1, 1, 4, 4, 
        4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 1, 1, 2, 
        2, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), .Names = "value")), 
    <environment>), class = "igraph")

I don't understand what the problem is.

Answer 1

When you search "degree" you can find two kinds of degree functions. In my case, I can see like this,

?degree

Help on topic 'degree' was found in the following packages:
Compute the Degree Centrality Scores of Network Positions
(in package sna in library C:/Program Files/R/R-3.3.1/library)
Degree and degree distribution of the vertices
(in package igraph in library C:/Program Files/R/R-3.3.1/library)

The degree function in sna package do not have "mode" argument but igraph has it.

So you can make your R script to recoginize where it is from using " :: ".

> deg <- degree(net, mode="all")
Error in degree(net, mode = "all") : unused argument (mode = "all")
> deg <- igraph::degree(net, mode="all")
> 

Enjoy R !!

Answer 2

The problem is a conflict between several libraries that you loaded above. The solution is defined in the command of the degree function of being called well is of igraph .

You specify it as follows: library_name :: function_name

In your case, the library_name value is igraph and function_name is degree , so your code should look like this:

deg <- igraph::degree (net, mode = "all")

and it works.

This method is very useful, but it should not create the conflict (same function name in two different packages), so specify the package to use with the :: .

Example:

The library ade4 contains a function named within and the base environment of R already contains a function within . Of course, the within of ade4 has a different action than within of base .

So if in my work environment, I have both libraries loaded ( base and ade4 ) and I want to use the function within , I will have a R execution conflict. This is due to 2 functions having the same name and R not knowing which library you are wanting to use. In this case you have to specify the library concerned.

Here, as we know the library, we do not want to try to detach the one that uses with detach("package:ade4") .

While writing the code, one knows the library which you want to use for the function, so without detaching the package, you would do one of these:

• To execute the within function of base then: base::within()

• To execute the within function of ade4 then: ade4::within()

I hope you have answered and explained well.