The sparrow.shiny package provides an interactive shiny applications
that enables users to explore the results of a gene set enrichment
analysis performed using the
sparrow
Although this is a standalone package, it’s really only used as an “enhancement” to the sparrow package itself, as well as providing shiny modules to the FacileAnalysis package, too.
All that of that is to say: there isn’t much end-user stuff here to play with.
More thorough documentation of the shiny application will be provided in the near future in the form of a vignette, or more likely a screen cast.
In the meantime, this will just have to get you started:
vm <- sparrow::exampleExpressionSet(dataset = 'tumor-vs-normal', do.voom = TRUE)
gdb <- sparrow::exampleGeneSetDb()
sr <- sparrow::seas(gdb, vm, vm$design, "tumor", methods = c("camera", "fry"))
sparrow.shiny::explore(sr)The explore function will launch the application and load it with the
SparrowResult object produced by the call to the sparrow::seas()
function. You can then explore the results of the “camera” or “fry”
analysis through there.
Users can serialize SparrowResult objects to *.rds files on their
filesystem, which can also be loaded individually once the application
is launched.
Analysts can simply launch the sparrow.shiny::explore() application
from their workstation, however these applications can also be deployed
to a shiny server.
The inst/docker folder provides examples of how to
containerize and deploy this application in different contexts.
The Dockerfile-base creates a docker
image that, when run, launches the shiny app on
http://container.ip/sparrow (ie. http://localhost/sparrow).
The Dockerfile-shinyproxy creates
an image that can be deployed via a ShinyProxy
server.
Notes on setting up a ShinyProxy server on AWS are provided in the
aws-ubuntu-deployment.md file.
The sparrow suite of package will soon be submitted to bioconductor and
installable via the recommended BiocManager mechanism. In the
meantime, these packages can be installed like so:
# install.packages("remotes")
remotes::install_github("lianos/sparrow.shiny")