Input and Output Substitution Parameters

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 report or to include download links to these files. Substitutions take the form of: ${param} where 'param' is the substitution.

Valid Substitutions: 
input_dataLabKey Server automatically reads your input dataset (a tab-delimited table) into the data frame called labkey.data. For tighter control over the method of data upload, or to modify the parameters of the read.table function, you can perform the data table upload yourself:
labkey.data <- read.table("${input_data}", header=TRUE);
labkey.data;
imgout: <name>An image output file (such as jpg, png, etc.) that will be displayed as a Section of a report on the LabKey Server. The 'imgout:' prefix indicates that the output file is an image and the <name> substitution identifies the unique image produced after you call dev.off(). The following script displays a .png image in a report:
png(filename="${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();
tsvout: <name>A TSV text file that is displayed on LabKey Server as a section within a report. No downloadable file is created. For example:
write.table(labkey.data, file = "${tsvout:tsvfile}", sep = "t", 
qmethod = "double");
txtout: <name>A text file that is displayed on LabKey Server as a section within a report. No downloadable file is created. A CSV example:
write.csv(labkey.data, file = "${txtout:csvfile}");
pdfout: <name>A PDF output file that can be downloaded from the LabKey Server.
pdf(file="${pdfout:labkeyl_pdf}");
plot(c(rep(25,100), 26:75), c(1:100, rep(1, 50)), ylab= "L", xlab="LabKey",
xlim= c(0, 100), ylim=c(0, 100), main="LabKey in R");
dev.off();
psout: <name>A postscript output file that can be downloaded from the LabKey Server.
postscript(file="${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();
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:
write.table(labkey.data, file = "${fileout:tsvfile}", sep = "t", qmethod = "double", col.names=NA);
 Another example shows how to send the output of the console to a file:
options(echo=TRUE);
sink(file = "${fileout:consoleoutput.txt}");
labkey.data;
htmlout: <name>A text file that is displayed on LabKey Server as a section within a report. 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>"
)
write(txt, file="${htmlout:output}");
svgout: <name>An svg file that is displayed on LabKey Server as a section within a report. htmlout can be used to render svg outpust as well, however, using svgout will generate a more appropriate thumbnail image for teh report. No downloadable file is created:
svg("${svgout: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.

Implicit variables: 
labkey.dataThe data frame which the input dataset is automatically read into. The code to generate the data frame is:
labkey.data <- read.table("${input_data}", header=TRUE, sep="t",
quote="", comment.char="")
labkey.url.pathThe 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.baseThe 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.paramsThe list of parameters on the current URL. The parameters are represented as a list of key / value pairs.
labkey.user.emailThe email address of the current user

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();

Additional Reference

Documentation and tutorials about the R language can be found at the R Project website.

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