The reports directory holds different kinds of reports and associated configuration files which determine how the reports are surfaced in the user interface.

Below we'll make an R report script that is associated with the PeptidesWithCounts query (created in the previous step).

  • In the reports/ directory, create the following subdirectories: schemas/ms2/PeptidesWithCounts, and a file named "Histogram.r", as shown below:
reportDemo │ module.properties └───resources    ├───queries    │ └───ms2    │ │ PeptideCounts.sql    │ │ PeptidesWithCounts.sql    │ │    │ └───Peptides    │ High Prob Matches.qview.xml    │    ├───reports    │ └───schemas    │ └───ms2    │ └───PeptidesWithCounts    │ Histogram.r    │    └───views

  • Open the Histogram.r file, enter the following script, and save the file. (Note that .r files may have spaces in their names.)
png(
filename="${imgout:labkeyl_png}",
width=800,
height=300)

hist(
labkey.data$fractionaldeltamass,
breaks=100,
xlab="Fractional Delta Mass",
ylab="Count",
main=NULL,
col = "light blue",
border = "dark blue")

dev.off()

Report Metadata

Optionally, you can add associated metadata about the report. See Modules: Report Metadata.

Test your SQL Query and R Report

  • Go to the Query module's home page ( (Admin) > Go to Module > Query). Note that the home page of the Query module is the Query Browser.
  • Open the ms2 node, and see your two new queries in the user-defined queries section.
  • Click on PeptidesWithCounts and then View Data to run the query and view the results.
  • While viewing the results, you can run your R report by selecting (Reports) > Histogram.

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