Determine Available Graphing Functions

Test Machine Capabilities. Before reading this section further, figure out whether you need to worry about its contents. Execute the following script in the R script builder:

if(!capabilities(what = "jpeg") || !capabilities(what="X11"))
warning("You cannot use the jpeg() function on your LabKey Server");
if(!capabilities(what = "png") || !capabilities(what="X11"))
warning("You cannot use the png() function on your LabKey Server");
If this script outputs both warnings, you’ll need to avoid both jpeg() and png() functions. If you do not receive warnings, you can ignore the rest of this section.

Why Don't png() and jpeg() Work? On Unix, jpeg() and png() rely on the x11() device drivers. These are unavailable when R is installed on a "headless" Unix server.

If png() and jpeg() Don't Work, What Are My Options?. You have two categories of options:

  1. Ask your admin to install a display buffer on the server such that it can access the appropriate device drivers.
  2. Avoid jpeg() and png(). There are currently three choices for doing so: Cairo(), GDD() and bitmap().
Which Graphics Function Should I Use? If you are working on a headless server without an installed display buffer, you will need to use Cairo(), GDD() or bitmap(). There are trade-offs for all options. If you use Cairo or GDD, your admin will need to install an additional graphics package. The Cairo package is based upon libraries undergoing continued development and maintenance, unlike the GDD package. Cairo does not require the use of Ghostscript to produce graphics, as does the bitmap() function. However, Cairo() fails to provide all graphics functions on all machines, so you will need to test its capabilities. GDD may provide functions unavailable in Cairo, depending on your machine setup.

Warning: LabKey R usually runs in batch mode, so any call to plot() must be preceded by a call to open the appropriate device (e.g., jpeg() or pdf()) for output. When R runs in its ordinary, interpreted/interactive mode, it opens an appropriate output device for graphics for you automatically. LabKey R does not do this, so you will need to open an output device for graphics yourself. Identifying appropriate devices and function calls is tricky and covered in this section.

Strategy #1: Use the Cairo and/or GDD Packages

You can use graphics functions from the GDD or Cairo packages instead of the typical jpeg() and png() functions.

There are trade-offs between GDD and Cairo. Cairo is being maintained, while GDD is not. GDD enables creation of .gif files, a feature unavailable in Cairo. You will want to check which image formats are supported under your installation of Cairo (this writer's Windows machine can not create .jpeg images in Cairo). Execute the following function call in the script-builder window to determine formats supported by Cairo on your machine:

Cairo.capabilities();
The syntax for using these packages is simple. Just identify the “type” of graphics output you desire when calling GDD or Cairo. The substitution parameters used for file variables are not unique to Cairo/GDD and are explained in subsequent sections.

#   Load the Cairo package, assuming your Admin has installed it:
library(Cairo);
# Identify which "types" of images Cairo can output on your machine:
Cairo.capabilities();
# Open a Cairo device to take your plotting output:
Cairo(file="${imgout:labkeyl_cairo.png}", type="png");
# Plot a LabKey L:
plot(c(rep(25,100), 26:75), c(1:100, rep(1, 50)), ylab= "L", xlab="LabKey",
xlim= c(0, 100), ylim=c(0, 100), main="LabKey in R");
dev.off();

# Load the GDD package, assuming your Admin has installed it:
library(GDD);
# Open a GDD device to take your plotting output:
GDD(file="${imgout:labkeyl_gdd.jpg}", type="jpeg");
# Plot a LabKey L:
plot(c(rep(25,100), 26:75), c(1:100, rep(1, 50)), ylab= "L", xlab="LabKey",
xlim= c(0, 100), ylim=c(0, 100), main="LabKey in R");
dev.off();

Strategy #2: Use bitmap()

It is possible to avoid using either GDD or Cairo for graphics by using bitmap(). Unfortunately, this strategy relies on Ghostscript, reportedly making it slower and lower fidelity than other options. Instructions for installing Ghostscript are available here.

NB: This method of creating jpegs has not been thoroughly tested.

Calls to bitmap will specify the type of graphics format to use:

bitmap(file="${imgout:p2.jpeg}", type = "jpeg");

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