seuratvis

Visualise data contained in a Seurat object

This package is very early stages and under development. Bug reports and feature suggestions are welcome!

install package

Either install the package or clone a version for development

install the package

Could use remotes to install the master branch as a package. This method should take care of the dependencies.

remotes::install_github(repo='ChristopherBarrington/seuratvis')

Or use the dev branch if you are brave.

remotes::install_github(repo='ChristopherBarrington/seuratvis', ref='dev')

possible errors

If a package binary is unavailable for your installed R version, you may get an error something like:

Error: (converted from warning) package 'shinydashboardPlus' was built under R version 3.6.3

This can be avoided with:

install.packages('shinydashboardPlus', type='source')

dqshiny may not be available on CRAN so should be installed with the following:

remotes::install_github('daqana/dqshiny')

clone this repository

Make a local copy of the repository using git clone ChristopherBarrington/seuratvis. Now use R to load the package and run the shiny app (you will need to install all of the dependencies manually, sorry!).

setwd('/path/to/seuratvis/containing/directory')
require(devtools) || install.packages('devtools')
devtools::load_all('seuratvis', export_all=FALSE)

run package

The package expects the current workspace to contain:

• at least one Seurat object in the global- or a sub-environment. The global environment and any environments within global are searched for Seurat object which can be selected from the configure tab.
  • it will not be happy if there is not at least one!

seuratvis()

The app should now open a new window.

developments

• loading seurat objects by uploading a dataset (maybe)
• all the stuff in the Issues