Visualization of static and dynamic networks on R, part 2

In the first part :

• network visualization: why? how?
• visualization parameters
• best practices - aesthetics and performance
• data formats and preparation
• description of the data sets used in the examples
• getting started with igraph

In this part: colors and fonts in graphs R.

Brief Introduction I: Colors in Graphs R

Colors are beautiful, but more importantly, they help to distinguish between object types, property gradations. Most R functions can use color names , RGB or hex values . In a simple basic graph, R below x and y are the coordinates of points, pch is the symbol for points, cex is the size of a point, and col is color. To find out what are the options for plotting graphs in R, run the command ?par .

 plot(x=1:10, y=rep(5,10), pch=19, cex=3, col="dark red") points(x=1:10, y=rep(6, 10), pch=19, cex=3, col="557799") points(x=1:10, y=rep(4, 10), pch=19, cex=3, col=rgb(.25, .5, .3)) 

As you can see, RGB here varies from 0 to 1. This is the default setting for R, but you can set the range from 0 to 255 using the rgb(10, 100, 100, maxColorValue=255) command rgb(10, 100, 100, maxColorValue=255) .

You can set the transparency of the element using the alpha parameter (from 0 to 1):

 plot(x=1:5, y=rep(5,5), pch=19, cex=12, col=rgb(.25, .5, .3, alpha=.5), xlim=c(0,6)) 

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If you are using a hexadecimal color representation, you can set the transparency factor using the adjustcolor from the grDevices package. For fun, let's also paint the background of the graphics in gray using the par() function to set the graphics settings.

 par(bg="gray40") col.tr <- grDevices::adjustcolor("557799", alpha=0.7) plot(x=1:5, y=rep(5,5), pch=19, cex=12, col=col.tr, xlim=c(0,6)) 

If you plan to use the built-in color names, here’s how you can get them all:

 colors() # List all named colors grep("blue", colors(), value=T) # Colors that have "blue" in the name 

In most cases, we need or a few contrasting colors, or shades of the same color. R has a built-in palette function that can generate this. For example:

 pal1 <- heat.colors(5, alpha=1) # 5 colors from the heat palette, opaque pal2 <- rainbow(5, alpha=.5) # 5 colors from the heat palette, transparent plot(x=1:10, y=1:10, pch=19, cex=5, col=pal1) 

 plot(x=1:10, y=1:10, pch=19, cex=5, col=pal2) 

We can also create our own gradients using the colorRampPalette . Note that colorRampPalette returns a function that can be used to generate as many colors from this palette as needed.

 palf <- colorRampPalette(c("gray80", "dark red")) plot(x=10:1, y=1:10, pch=19, cex=5, col=palf(10)) 

To add transparency to the colorRampPalette , you need to use the alpha=TRUE parameter:

 palf <- colorRampPalette(c(rgb(1,1,1, .2),rgb(.8,0,0, .7)), alpha=TRUE) plot(x=10:1, y=1:10, pch=19, cex=5, col=palf(10)) 

Finding a good color combination is not an easy task, and the built-in R palettes are quite limited. Fortunately, other packages solve this problem:

 # If you don't have R ColorBrewer already, you will need to install it: install.packages("RColorBrewer") library(RColorBrewer) display.brewer.all() 

This package has one main function - brewer.pal . In order to use it, you only need to select the desired palette and the number of colors. Let's take a look at some RColorBrewer palettes:

 display.brewer.pal(8, "Set3") 

 display.brewer.pal(8, "Spectral") 

 display.brewer.pal(8, "Blues") 

Using RColorBrewer palettes in graphs:

 pal3 <- brewer.pal(10, "Set3") plot(x=10:1, y=10:1, pch=19, cex=4, col=pal3) 

Brief Introduction II: Fonts in Graphs R

Using different fonts in R charts may require some effort. This is especially true for Windows users; Mac and Linux users are likely to safely skip this section.

In order to import fonts from OS to R, we use the extrafont package:

 install.packages("extrafont") library(extrafont) # Import system fonts - may take a while. font_import() fonts() # See what font families are available to you now. loadfonts(device = "win") # use device = "pdf" for pdf plot output. 

Now fonts are available, and you can do something like this:

 library(extrafont) plot(net, vertex.size=30) plot(net, vertex.size=30, vertex.label.family="Arial Black" ) 

When you save graphics as PDF files, you can also install fonts:

 # First you may have to let R know where to find ghostscript on your machine: Sys.setenv(R_GSCMD = "C:/Program Files/gs/gs9.10/bin/gswin64c.exe") # pdf() will send all the plots we output before dev.off() to a pdf file: pdf(file="ArialBlack.pdf") plot(net, vertex.size=30, vertex.label.family="Arial Black" ) dev.off() embed_fonts("ArialBlack.pdf", outfile="ArialBlack_embed.pdf")