HW3 Cheat Sheet

This is a cheat sheet for the third homework. It works through each step in R.

First, you need the following packages.

Code

library(igraph)
library(readr)
library(RColorBrewer)

1. Toy Graph

First, we are going to construct the toy graph. We can make an edge list based on how the nodes are connected to one another.

And make a vector of node colors that correspond to each of the nodes.

Code

edges <- c(1,2, 1,3, 1,6, 2,3, 2,5, 3,4, 3,5, 6,2)


colors <- c("yellow", "red", "green", "yellow", "red", "green")

Now we can use the graph function in igraph to read the graph into an igraph object and assign the color in the function.

Code

t.g <- graph(edges, directed=T)

plot(t.g, vertex.color=colors, edge.arrow.size=.5)

You could also assign colors as vertex attribute in the igraph object. Then you don’t have to. assign colors inside the graph function.

Code

V(t.g)$color <- colors

plot(t.g, edge.arrow.size=.5)

2. Game of Thrones

First we load the data from the Game of Thrones book and inspect.

Code

stormofswords <- read_csv("data/stormofswords.csv") 

head(stormofswords)

# A tibble: 6 × 3
  Source Target  Weight
  <chr>  <chr>    <dbl>
1 Aemon  Grenn        5
2 Aemon  Samwell     31
3 Aerys  Jaime       18
4 Aerys  Robert       6
5 Aerys  Tyrion       5
6 Aerys  Tywin        8

We can see that this is a weighted edgelist in a data frame. So, we can use graph_from_data_frame to make an igraph object. If we return the graph name, we can see the graph summary. We can also see an initial plot.

Code

thr.g <- graph_from_data_frame(stormofswords)

#Let's take a peek at the graph summary

thr.g

IGRAPH db58165 DN-- 107 352 -- 
+ attr: name (v/c), Weight (e/n)
+ edges from db58165 (vertex names):
 [1] Aemon  ->Grenn     Aemon  ->Samwell   Aerys  ->Jaime     Aerys  ->Robert   
 [5] Aerys  ->Tyrion    Aerys  ->Tywin     Alliser->Mance     Amory  ->Oberyn   
 [9] Arya   ->Anguy     Arya   ->Beric     Arya   ->Bran      Arya   ->Brynden  
[13] Arya   ->Cersei    Arya   ->Gendry    Arya   ->Gregor    Arya   ->Jaime    
[17] Arya   ->Joffrey   Arya   ->Jon       Arya   ->Rickon    Arya   ->Robert   
[21] Arya   ->Roose     Arya   ->Sandor    Arya   ->Thoros    Arya   ->Tyrion   
[25] Balon  ->Loras     Belwas ->Barristan Belwas ->Illyrio   Beric  ->Anguy    
[29] Beric  ->Gendry    Beric  ->Thoros    Bran   ->Hodor     Bran   ->Jojen    
+ ... omitted several edges

Code

#Initial plot

plot(thr.g)

The plot is a bit messy and it is hard to make much sense of it, so let’s add some additional information.

We can add the houses as attributes

Code

load("~/Documents/GitHub/sna_course/week_3_visualization/week3_visualization/data/got_att.rda") #This point to where attribute file is located

#Inspect thing

head(got_att)

    names degree house
1   Aemon      5     0
2   Aerys      4     0
3 Alliser      3     0
4   Amory      1     0
5    Arya     19     2
6   Balon      6     0

We can see there are names, degree, and the house (0=“Other”, 1=“Lannister”, 2=“Stark”, 3=“Tagaryen”, 4=“Baratheon”)

Let’s store those in the vertices

And plot with the setting vertex color by house and vertex size by degree, and edge width by weight

Code

V(thr.g)$degree <- got_att$degree

V(thr.g)$house <- got_att$house

plot(thr.g, vertex.color=V(thr.g)$house+1, vertex.size=V(thr.g)$degree/2, edge.arrow.size=.1, edge.width=E(thr.g)$Weight/10,
     layout=layout_with_kk)

It might be nice to include a legend. The Moody and Light 2020 tutorial describes how to accomplish that.

Start with the RColorBrewer Package and index the colors. Then connect the colors to the house attribute as a factor and plot.

Code

library(RColorBrewer)

#Index the colors

pal <- brewer.pal(5, "Accent")

#Connect the colors to the house attribte as a factor

vertex.col <- (pal[as.numeric(as.factor(vertex_attr(thr.g, "house")))])

#plot...note I adjust the color by making more transparent (alpha=)

plot(thr.g, vertex.color=adjustcolor(vertex.col, alpha=.75), vertex.label=NA, vertex.size=V(thr.g)$degree/2, edge.arrow.size=.1, 
     edge.width=E(thr.g)$Weight/10, layout=layout_with_kk)

#Add legend (see https://www.rdocumentation.org/packages/graphics/versions/3.6.2/topics/legend)

legend("topleft", title="House", bty = "n", #set location, legend title, and box type
       legend=c("Other","Lannister", "Stark", "Tagaryen", "Baratheon"), #legend words
       fill=pal, border=NA) #fill of circles and we don't need a border