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Last year I published the above graphic, which then got converted into the below for the book London: The Information Capital. I have had many requests for the code I used to create the plot so here it is!

The data shown is the Office for National Statistics flow data. See here for the latest version. The file I used for the above can be downloaded here (it is >109 mb uncompressed so you need a decent computer to load/plot it all at once in R). You will also need this file of area (MSOA) codes and their co-ordinates. The code used is pasted below with comments above each segment. Good luck!
 library(plyr) library(ggplot2) library(maptools) 

Load the flow data required – origin and destination points are needed. See above for where you can get the table used here.
 input<-read.table("wu03ew_v1.csv", sep=",", header=T) 
We only need the first 3 columns of the above
 input<- input[,1:3] names(input)<- c("origin", "destination","total") 

The UK Census file above didn't have coordinates just area codes. Here is a lookup that provides those. See above for download.
 centroids<- read.csv("msoa_popweightedcentroids.csv") 

Lots of joining to get the xy coordinates joined to the origin and then the destination points.
 or.xy<- merge(input, centroids, by.x="origin", by.y="Code") names(or.xy)<- c("origin", "destination", "trips", "o_name", "oX", "oY") dest.xy<- merge(or.xy, centroids, by.x="destination", by.y="Code") names(dest.xy)<- c("origin", "destination", "trips", "o_name", "oX", "oY","d_name", "dX", "dY") 

Now for plotting with ggplot2.This first step removes the axes in the resulting plot.
 xquiet<- scale_x_continuous("", breaks=NULL) yquiet<-scale_y_continuous("", breaks=NULL) quiet<-list(xquiet, yquiet) 

Let's build the plot. First we specify the dataframe we need, with a filter excluding flows of <10
 ggplot(dest.xy[which(dest.xy\$trips>10),], aes(oX, oY))+ 
The next line tells ggplot that we wish to plot line segments. The "alpha=" is line transparency and used below
 geom_segment(aes(x=oX, y=oY,xend=dX, yend=dY, alpha=trips), col="white")+ 
Here is the magic bit that sets line transparency - essential to make the plot readable
 scale_alpha_continuous(range = c(0.03, 0.3))+ 
Set black background, remove axes and fix aspect ratio
 theme(panel.background = element_rect(fill='black',colour='black'))+quiet+coord_equal() 

We used ggave() to export from R and then we imported the pdf into Illustrator to produce the final graphic for print...