knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
The sparrow.shiny
package provides an interactive shiny applications that
enables users to explore the results of a gene set enrichment analysis performed
using the sparrow
Although this is a standalone package, it's really only used as an "enhancement" to the sparrow package itself, as well as providing shiny modules to the FacileAnalysis package, too.
All that of that is to say: there isn't much end-user stuff here to play with.
More thorough documentation of the shiny application will be provided in the near future in the form of a vignette, or more likely a screen cast.
In the meantime, this will just have to get you started:
vm <- sparrow::exampleExpressionSet(dataset = 'tumor-vs-normal', do.voom = TRUE) gdb <- sparrow::exampleGeneSetDb() sr <- sparrow::seas(gdb, vm, vm$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")
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