Getting started

Install

Install all the packages in the natverse by running:

if(!requireNamespace('remotes', quietly=TRUE)) {install.packages('remotes')}
remotes::install_github("natverse/natverse", dependencies=TRUE)

Run

To load the core natverse and make it available in your current R session:

library(natverse)

You can check everything is working with some simple plots:

# plot some test data (?kcs20 for details)
# Drosophila Kenyon cells processed from raw data at http://flycircuit.tw
head(kcs20)
open3d()
plot3d(kcs20, col=type)
# get help
?nat

To find our more, explore our resources for learning the natverse.

Update

To update all natverse packages (and their dependencies):

library(natverse)
# see what needs updating
natverse_update()
# actually update
natverse_update(update = TRUE)
# ... or if you don't want to answer any yes/no questions
natverse_update(update = TRUE, upgrade='always')

Troubleshooting

If you have any installation issues, some general tips:

  • make sure that you have started a clean R session
  • make sure that you have recent R (>=3.6.0 recommended, R>=3.3.0 at a minimum)
  • try updating installed packages (update.packages(ask=F) will update everything)

Still no luck?

  • most install issues will be general R issues rather than anything specific to the natverse, so Google is your friend.
  • Search the nat-user google group.
  • … or use it to ask for help.

By: [Gregory Jefferis]