Getting started

Installation

The natverse runs on top of R. If you have never installed R see the First time install and Step by Step illustrated guide at the bottom of this page.

Basic Install

Install core natverse packages to get started by doing

install.packages("natmanager")
natmanager::install('core')

Full Install

Install all the packages in the natverse by running:

install.packages("natmanager")
natmanager::install('natverse')

You may need to make a GitHub account and personal access token (GITHUB_PAT) if you have not done this previously. See the GitHub Rate limiting and Step by Step Installation Guide sections below.

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

GitHub Rate limiting

Unfortunately installing the full natverse suite makes many calls to the GitHub API, which is rate limited unless you have a GitHub account and present a GITHUB_PAT authentication token. The natmanager package will attempt to use a built-in PAT if you do not have one. However, if multiple users are installing the natverse simultaneously, you may get errors like

Using github PAT from envvar GITHUB_PAT
Error: Failed to install 'unknown package' from GitHub:
  HTTP error 401.
  Bad credentials
  Rate limit remaining: 56/60
  Rate limit reset at: 2020-02-27 19:21:26 UTC

To avoid these errors, do

natmanager::check_pat()

and this will guide you through the process of obtaining your own GITHUB_PAT and telling R about it. See also the illustrated guide below.

Other install issues

If you have any installation issues, some general tips:

  • Start a clean R session
  • Start a clean R session if you had to update natmanager
  • 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.

First time install - Prerequisites

To install this package you need to have R and RStudio installed. Detailed instructions for each operating system are given below. You will also need a valid GitHub account to install the full suite of natverse packages. You will be prompted to do this by the natmanager package, but we recommend following the illustrated Step by Step Installation Guide.

Mac OS X

  1. Install R from here: r-installation

  2. Install RStudio, from here: RStudio-installation

  3. Start RStudio from Launchpad

  4. To use the rgl package for 3D visualisation you may also need to install the Xquartz X11 system, which is also available by following links from the CRAN Mac OS X page.

Windows

  1. Install R from here: r-installation

  2. Install RStudio, for Windows from here: RStudio-installation

  3. Start RStudio from Programs menu

Linux (Ubuntu)

  1. Install R, in terminal type below:

    sudo apt-get install libopenblas-base r-base

  2. Install RStudio, in terminal type below:

    sudo apt-get install gdebi
cd ~/Downloads
wget https://download1.rstudio.org/rstudio-xenial-1.1.419-amd64.deb
sudo gdebi rstudio-xenial-1.1.419-amd64.deb

  3. Start RStudio, in terminal type below:

    rstudio

Step by Step Installation Guide

By: Sridhar Jagannathan & Gregory Jefferis
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