Comment Syntax
Inline Syntax (Deprecated)

Syntax reference

Your R script uses input substitution parameters to generate the names of input files and to import data from your chosen Dataset Grid. It then uses output substitution parameters to either directly place image/data files in your View or to include download links to these files in your View. Substitutions consist of a comment line in the form of: #${param:filename} where 'param' is the substitution and 'filename' is the input/output filename. 'filename' is then used in the script line right below the comment line to reference the input/output file.

Valid substitutions

input_data:<name>	The input dataset, a tab-delimited table. LabKey Server automatically reads your chosen dataset into a data frame called: `labkey.data`. If you desire tighter control over the method of data upload, you can perform the data upload yourself. The 'input_data:' prefix indicates that the data file for the grid and the <name> substitution can be set to any non empty value: # ${input_data:inputTsv} labkey.data <- read.table("inputTsv", header=TRUE, sep="\t") labkey.data
imgout:<name>	An image output file (such as jpg, png, etc.) that will be displayed as a Section of a View on the LabKey Server. The 'imgout:' prefix indicates that the output file is an image and the <name> substitution identifies the unique image produced after you call `dev.off()`. The following script displays a .png image in a View: # ${imgout:labkeyl.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:<name>	A TSV text file that is displayed on LabKey Server as a Section within a View. No downloadable file is created. For example: # ${tsvout:tsvfile} write.table(labkey.data, file = "tsvfile", sep = "\t", qmethod = "double", col.names=NA)
txtout:<name>	A text file that is displayed on LabKey Server as a Section within a View. No downloadable file is created. A CSV example: # ${txtout:csvfile} write.csv(labkey.data, file = "csvfile")
pdfout:<name>	A PDF output file that can be downloaded from the LabKey Server. The 'pdfout:' prefix indicates that the expected output is a pdf file. The <name> substitution identifies the unique file produced after you call `dev.off()`. # ${pdfout:labkeyl.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:<name>	A postscript output file that can be downloaded from the LabKey Server. The 'psout:' prefix indicates that the expected output is a postscript file. The <name> substitution identifies the unique file produced after you call `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:<name>	A file output that can be downloaded LabKey Server, and may be of any file type. For example, use `fileout` in the place of tsvout to allow users to download a TSV instead of seeing it within the page: # ${fileout:tsvfile} write.table(labkey.data, file = "tsvfile", sep = "\t", qmethod = "double", col.names=NA)
htmlout:<name>	A text file that is displayed on LabKey Server as a Section within a View. The output is different from the `txtout:` replacement in that no html escaping is done. This is useful when you have a report that produces html output. No downloadable file is created: 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:<name>	An svg file that is displayed on LabKey Server as a Section within a View. `htmlout` can be used to render svg outputs as well, however, using `svgout` will generate a more appropriate thumbnail image for the report. No downloadable file is created: # ${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.

labkey.data	The data frame which the input dataset is automatically read into. The code to generate the data frame is: # ${input_data:inputFileTsv} labkey.data <- read.table("inputFileTsv", header=TRUE, sep="\t", quote="", comment.char="")
labkey.url.path	The path portion of the current URL which omits the base context path, action and URL parameters. The path portion of the URL: `http://localhost:8080/labkey/study/home/test/begin.view` would be: `/home/test/`
labkey.url.base	The base portion of the current URL. The base portion of the URL: `http://localhost:8080/labkey/study/home/test/begin.view` would be: `http://localhost:8080/labkey/`
labkey.url.params	The list of parameters on the current URL. The parameters are represented as a list of key / value pairs.
labkey.user.email	The email address of the current user

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

<replacement>:regex(<expression>)

The following example will find all files generated by the script with the extension : '.gct'. If any are found
they will be assigned and rendered to the replacement parameter (in this case as a download link).

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

Syntax reference

Your R script uses input substitution parameters to generate the names of input files and to import data from your chosen Dataset Grid. It then uses output substitution parameters to either directly place image/data files in your View or to include download links to these files in your View. Substitutions take the form of: ${param} where 'param' is the substitution.