从 mvbutils R-package 控制食物网图中的图布局

Question

I would like to visualize how functions in my own R package depend on each other. For this purpose I use the foodweb() function from the mvbutils package.

I can get the right functional dependencies out without a problem but the plot looks a bit messy, with lines crossing each other and function names not aligned vertically or horizontally.

Is there a way to control the layout of the plot similar to the way this works in the igraph package?

Example

dirPath <- "~/dev/stackoverflow/46910042"
setwd(dirPath)

## Download example Package
urlPackage <- "https://github.com/kbroman/qtlcharts/archive/master.zip"
download.file(urlPackage, destfile = "master.zip")
unzip("./master.zip", exdir = dirPath, overwrite = TRUE)

## Install or load mcbutils
if (!require(mvbutils)) install.packages("mvbutils")
thefiles = list.files(path = "./qtlcharts-master/R/", full.names = TRUE)
thefiles
## Now we load all the package files into memory, so we can have 
## foodweb generate a map of the package functions.
sapply(thefiles, source)

## Generate plot 
par(mar = rep(0.1, 4))
foodweb(border = TRUE, boxcolor = "pink", lwd = 1.5, cex = 0.8)

Plot Output:

Answer 1

Michael,

One option is to look behind the curtains of foodweb. The mvbutils::foodweb function returns an object of (S3) class foodweb . This has three components:

• funmat a matrix of 0s and 1s showing what (row) calls what (column). The dimnames are the function names.
• x shows the x-axis location of the centre of each function's name in the display, in par("usr") units
• level shows the y-axis location of the centre of each function's name in the display, in par("usr") units.

thus one approach we can take is to call foodweb but tell it not to create a plot rather return a foodweb object. This then allows us to manipulate the data directory or via graphics::plot() externally of the defaults provided by the mvbutils::foodweb() function.

Why? Well, to do what you suggest my sense is three options exist:

• You can either play with mvbutils::foodweb() parameters.
• Work with data structure returned with another plotting package.
• Use graphics::par() and graphics::plot to manipulate the plot size and attributes of the foodweb structure returned.

It would be great to know your preference. Excluding, that my sense was to provide a base example:

Plot Package Example

In the case of using graphics::plot , you need to go look at how you manipulate graphics:par . par() allows you to set or query graphical parameters. For example, if we want to clean up the function plot you might choose to modify the grahics::par() fin parameter to increase the figure region dimensions, (width, height), in inches. A simple example but my sense it helps map out and demonstrate the options available to you.

## Generate plot
if (!require(qtlcharts)) install.packages("qtlcharts")

## Here we specify `asNamespace` to get the package internals
fw <- foodweb( where = asNamespace( "qtlcharts"),
               plotting = FALSE,
               )
#Display foodweb structure
str(fw)

# Expand plot figure region dimensions...
par(fin = c(9.9,7))
# Plot fw strucuture
plot(fw, 
     border = TRUE, 
     expand.xbox = 1,
     boxcolor = "pink", lwd = 1.5, cex = 0.8)

Plot Output example

Note that the function names are not spaced out. Note I cut the top and bottom white of plot here. In this case, you can play with the par constraints such as margin to get the plot you want.

Pruning your plot

Another option within the constraints of mvbutils::foodweb is to use the prune and rprune option to simplify your plots. These are super poweful and useful especially the regular expression version.

if (!require(qtlcharts)) install.packages("qtlcharts")
fw <- foodweb( where = asNamespace( "qtlcharts"),
               plotting = FALSE)

str(fw)
par(fin = c(9.9,7))
plot(fw, 
     border = TRUE, 
     expand.xbox = 1,
     boxcolor = "pink", lwd = 1.5, cex = 0.8)

fw <- foodweb( where = asNamespace( "qtlcharts"),
               rprune = "convert_", ## search on `convert_` to negate use `~convert_`
               plotting = FALSE)
str(fw)
par(fin = c(9.9,7))
plot(fw, 
     border = TRUE, 
     expand.xbox = 1,
     boxcolor = "pink", lwd = 1.5, cex = 0.8)

Hoping the above information points you in the right direction. T.

Answer 2

Because of the fact that there are many data, connections etc, the plot is squeezed in order to fit in the screen, hence it becomes messy.

What I would suggest is to save it in a PDF or PNG with big enough width and Height and then you can zoom in. This will save you a lot of time. EG

## Generate plot 
pdf( "mygraph.pdf", width = 50, height = 80 )
par(mar = rep(0.1, 4))
foodweb(border = TRUE, boxcolor = "pink", lwd = 1.5, cex = 0.8)
dev.off()

In addition, you can play with the plot options of foodweb .

Hope it helps.