Acquacotta

R Shiny App to display Run Reports generated by the OICR SeqWare pipeline.

Installing

Requirements

Requires R 3.3+ and the libv8-dev package

While in the base directory, execute code in the R console:

devtools::install()

Before starting Acquacotta, ensure Run Report folders are accessible in the directory specified in the config file. Options that can be modified are:

• Location of Run Report folders
• Default plots to display
• Default metric to sort on

Running

R Console

Execute command below:

acquacotta::runAcquacotta()

Rscript

Run the command below and open the listed address in a Web Browser:

Rscript app.R

RStudio

Load the app.R file in RStudio and click the Run App button or press Command+Shift+Enter.

Shiny Server

See the official documentation for detailed description on hosting Shiny Apps. To host Acquacotta, make repository visible in the server path (by default /srv/shiny-server and configurable at /etc/shiny-server/shiny-server.conf).

Updating

To ensure Shiny Server correctly hosts an updated version of Acquacotta, change the modification time of the restart.txt file immediately after an update. On Linux, that can be done by running

touch restart.txt

Usage

• Use Select Run Report drop-down menu to select Run Report to load.
• Use Select Study to specify studies to display. By default, all studies are shown for a run.
• Use Select Lane to specify which lanes to display. By default, all lanes are shown for a run.
• Specific Libraries can be selected by clicking on the plotted bars. Information on selected Libraries is displayed under the Selections tab.
• Use Order By to specify on which metric to sort.
• Use Select Plots to specify which plots to render.
• Use Coverage slider to exclude libraries that lie outside of range.

Known Issues

• Clicking on Library bars randomly fails to select them
• The UI components cannot be tested, as plotly creates new id variables for each instance: rstudio/shinytest#174