Reference Dashboard for flowDashboard

This repo is a reference dashboard for the flowDashboard package: https://github.com/laderast/flowDashboard. It uses the GvHD dataset from flowStats.

You can see the reference dashboard in action here: https://tladeras.shinyapps.io/sampleFlowDashboard/

To run it, you will need to install the flowDashboard package:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install(c("flowCore", "flowWorkspace"), dependencies=TRUE)
install.packages("remotes")
remotes::install_github("laderast/flowDashboard")

flowDashboard modules take three different data objects as input (which are available in data/GvHD.rda)

• QCO - A qcFlowObject. A quality control object. These are sampled rows from each flowFrame in the dataset. You can build these objects from a GatingSet or a flowSet using QCOFromGatingSet().
• GO - A gatingObject. A object with cell counts of each population in the GatingSet percentages of each population in the GatingSet. There is also an imageDir that contains the gating provenance graphics for each Population/Sample. They are generated using GOFromGatingSet().
• PEO - A populationExpressionObject. Similar to the qcFlowObject, but it contains the markers that were not gating on for expression comparison across samples for associated populations. They are generated using PEOFromGatingSet.

There is a vignette detailing how each of these objects were built in docs/.

Data objects handle much of the display issues (populating fields in selectInputs, etc). Using simple methods on these objects, options such as Populations and Markers to display can be set (refer to the vignette for more information). Each object has a unique id to avoid namespace collisions, but this ID can be overridden.

Please report any bugs as issues in the main flowDashboard repo.