natverse / mouselightr

Bridge HHMI Janelia MouseLight Database and nat R Package

natverse

The natverse package is a wrapper for all of the commonly used NeuroAnatomy Toolbox packages. This is convenient both for package installation and for loading/attaching these packages without many calls to library().

See http://natverse.org for more details.

Installation

The recommended approach to install the full natverse is to use a helper package natmanager, which is available on CRAN. You can therefore do:

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

See http://natverse.org/install for more details.

Use

Once installed, you can load the natverse package:

library(natverse)
#> Loading required package: elmr
#> Loading required package: catmaid
#> Loading required package: httr
#> Warning: package 'httr' was built under R version 3.6.2
#> Loading required package: nat
#> Loading required package: rgl
#> Warning: package 'rgl' was built under R version 3.6.2
#> Registered S3 method overwritten by 'nat':
#>   method             from
#>   as.mesh3d.ashape3d rgl
#> 
#> Attaching package: 'nat'
#> The following object is masked from 'package:rgl':
#> 
#>     wire3d
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, union
#> Loading required package: nat.flybrains
#> Loading required package: nat.templatebrains
#> Loading required package: nat.nblast
# example 3D plot of some neurons
plot(kcs20, col=type)

Installation Details

Conflicts and Dependencies

The natverse package contains many packages and it is possible that there could be conflicts where functions in the natverse have the same name as another package.

natverse_conflicts()
#> ── Conflicts ─────────────────────────────────────────────────────────────── natverse_conflicts() ──
#> x nat::intersect() masks base::intersect()
#> x nat::setdiff()   masks base::setdiff()
#> x nat::union()     masks base::union()
#> x nat::wire3d()    masks rgl::wire3d()

You can always choose the correct version by prepending the specific package name e.g. nat::flip() will select the nat version rather than any other.

Updates

Once installed, you check the status of all natverse packages and their dependencies like so:

natverse_update()
#> 
#> The following packages are either locally installed or information about them is missing!
#> 
#>   blob, formattable, import, mockr, nycflights13, pingr, fafbsegdata, reticulate, nat
#> 
#> Please install them manually from their appropriate source locations
#> 
#> The following natverse dependencies are out-of-date, see details below:
#> 
#> We recommend updating them by running:
#> natverse_update(update=TRUE)
#> 
#> package         remote         local          source   repo                        status 
#> --------------  -------------  -------------  -------  --------------------------  -------
#> bit64           0.9-7.1        0.9-7          CRAN     https://cran.rstudio.com/   x      
#> data.table      1.13.0         1.12.8         CRAN     https://cran.rstudio.com/   x      
#> elmr            deb0e27df...   7a2be4537...   GitHub   natverse                    x      
#> ff              2.2-14.2       2.2-14         CRAN     https://cran.rstudio.com/   x      
#> flycircuit      1b7b48e29...   cc4594f47...   GitHub   natverse                    x      
#> git2r           0.27.1         0.26.1         CRAN     https://cran.rstudio.com/   x      
#> insectbrainr    6331b4df6...   8fef94a05...   GitHub   natverse                    x      
#> mouselightr     9c2ce1c31...   8e26b7702...   GitHub   natverse                    x      
#> nat.flybrains   28ff33213...   36c622a15...   GitHub   natverse                    x      
#> nat.jrcbrains   85ed4a791...   44c95667e...   GitHub   natverse                    x      
#> neuprintr       7403d3ce2...   8ab03b744...   GitHub   natverse                    x      
#> RCurl           1.98-1.2       1.98-1.1       CRAN     https://cran.rstudio.com/   x      
#> tibble          b4eec19dd...   3f4e5dfae...   GitHub   tidyverse                   x      
#> tidyr           1.1.0          1.0.3          CRAN     https://cran.rstudio.com/   x      
#> xfun            0.16           0.15           CRAN     https://cran.rstudio.com/   x      
#> XML             NA             3.99-0.3       CRAN     https://cran.rstudio.com/   x

You can then update like so:

natverse_update(update = TRUE)

However, if you are in a hurry and want to save time from the questions use like below:

natverse_update(update=TRUE, upgrade = 'always')

If want to upgrade the natverse package itself:

remotes::update_packages('natverse')

mouselightr's Issues

Unexported object imported by a ':::' call: ‘jsonlite:::null_to_na’

• creates a note in Rmd Check

rename package to mouselightr

• Rename package and repo to mouselightr rather than nat.mouselight

*Move to natverse's Github page

subset

Hi
I am trying to run the example code, and got this error. It looks like subset.hxsurf somehow broken.

amygdala.codes = mousebrain$neuropil_full_names[grepl("amygdala",mousebrain$neuropil_full_names, ignore.case = TRUE)]
plot3d(outline, col = "pink", alpha = 0.1)
plot3d(subset(mousebrain$Vertices, amygdala.codes), alpha = 0.5)
Error in subset.data.frame(mousebrain$Vertices, amygdala.codes) :
'subset' must be logical

My sessioninfo() output:

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] mouselightr_0.1.0 nat_1.10.1 rgl_0.100.54

loaded via a namespace (and not attached):
[1] igraph_1.2.5 Rcpp_1.0.4.6 knitr_1.28 magrittr_1.5
[5] nat.utils_0.5.1 xtable_1.8-4 R6_2.4.1 rlang_0.4.5
[9] filehash_2.4-2 fastmap_1.0.1 nabor_0.5.0 tools_3.6.3
[13] webshot_0.5.2 xfun_0.13 miniUI_0.1.1.1 htmltools_0.4.0
[17] crosstalk_1.1.0.1 yaml_2.2.1 digest_0.6.25 shiny_1.4.0.2
[21] later_1.0.0 codetools_0.2-16 htmlwidgets_1.5.1 promises_1.1.0
[25] manipulateWidget_0.10.1 mime_0.9 compiler_3.6.3 jsonlite_1.6.1
[29] httpuv_1.5.2 pkgconfig_2.0.3

enable GitHub pages

• for pkgdown website

Demo doesn't work

I got this when I tried the demo with R version 4.1.2. If anyone can help? Thanks!
outline = mouselight_read_brain(type = "outline")
Error in rep("+", percent/2) : invalid 'times' argument

Trun on Travis for this Repo

• Turn on travis for this repo

Should mouselight_neurons_by_brain_region be exported?

Currently not exported but it's used in examples e.g. http://natverse.org/mouselightr/reference/mouselight_neuron_info.html