• Input and Output Substitution Parameters
• Implicit Variables
• Cairo or GDD Packages
• Deprecated LabKey-specific Syntax

Input and Output Substitution Parameters

# ${labkey.data:inputTsv}
labkey.data <- read.table("inputTsv", header=TRUE, sep="\t");
labkey.data

# ${imgout:labkey1.png}
png(filename="labkeyl_png")
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()

# ${tsvout:tsvfile}
write.table(labkey.data, file = "tsvfile", sep = "\t", 
qmethod = "double", col.names="NA")

# ${txtout:tsvfile}
write.csv(labkey.data, file = "csvfile")

# ${pdfout:labkey1.pdf}
pdf(file="labkeyl_pdf")
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()

# ${psout:labkeyl.eps}
postscript(file="labkeyl.eps", horizontal=FALSE, onefile=FALSE)
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()

# ${fileout:tsvfile}
write.table(labkey.data, file = "tsvfile", sep = "\t",
  qmethod = "double", col.names=NA)

txt <- paste("<i>Click on the link to visit LabKey:</i>
  <a target='blank' href='http://www.labkey.org'>LabKey</a>")
# ${htmlout:output}
write(txt, file="output")

# ${svgout:output.svg}
svg("output.svg", width= 4, height=3)
plot(x=1:10,y=(1:10)^2, type='b')
dev.off()

Implicit Variables

Each R script contains implicit variables that are inserted before your source script. Implicit variables are R data types and may contain information that can be used by the source script.

# ${input_data:inputFileTsv} 
labkey.data <- read.table("inputFileTsv", header=TRUE, sep="\t",
  quote="", comment.char="")

Using Regular Expressions with Replacement Token Names

Sometimes it can be useful to have flexibility when binding token names to replacement parameters. This can be the case when a script generates file artifacts but does not know the file names in advance. Using the syntax: regex() in the place of a token name (where LabKey server controls the token name to file mapping) will result the following actions:

• Any script generated files not mapped to a replacement will be evaluated against the file's name using the regex.
• If a file matches the regex, it will be assigned to the replacement and rendered accordingly.

#${fileout:regex(.*?(\.gct))}

Cairo or GDD Packages

You may need to use the Cairo or GDD graphics packages in the place of jpeg() and png() if your LabKey Server runs on a "headless" Unix server. You will need to make sure that the appropriate package is installed in R and loaded by your script before calling either of these functions.

GDD() and Cairo() Examples. If you are using GDD or Cairo, you might use the following scripts instead:

library(Cairo);
Cairo(file="${imgout:labkeyl_cairo.png}", type="png");
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();

library(GDD);
GDD(file="${imgout:labkeyl_gdd.jpg}", type="jpeg");
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();

Deprecated LabKey-specific Syntax

Prior to release 18.1, file substitutions used a LabKey-specific syntax. The use of standard R syntax expected by RStudio as described above means the following syntax is deprecated and should be updated. You can also find this syntax within the R Report UI by selecting the Help tab, then Inline Syntax (Deprecated).

labkey.data <- read.table("${input_data}", header=TRUE);
labkey.data;

png(filename="${imgout:labkeyl_png}");
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();

write.table(labkey.data, file = "${tsvout:tsvfile}", sep = "\t", 
qmethod = "double");

write.csv(labkey.data, file = "${txtout:csvfile}");

pdf(file="${pdfout:labkeyl_pdf}");
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();

postscript(file="${psout:labkeyl_eps}", horizontal=FALSE, onefile=FALSE);
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();

write.table(labkey.data, file = "${fileout:tsvfile}", sep = "\t", qmethod = "double", col.names=NA);

options(echo=TRUE);
sink(file = "${fileout:consoleoutput.txt}");
labkey.data;

txt <- paste("<i>Click on the link to visit LabKey:</i>
   <a target='blank' href='http://www.labkey.org'>LabKey</a>")
write(txt, file="${htmlout:output}");

svg("${svgout:svg}", width= 4, height=3)
        plot(x=1:10,y=(1:10)^2, type='b')
        dev.off()

labkey.data <- read.table("${input_data}", header=TRUE, sep="\t",
            quote="", comment.char="")

Additional Reference

• Documentation and tutorials about the R language can be found at the R Project website
• Rlabkey package documentation: Data exchange between R and LabKey Server