diff --git a/README.Rmd b/README.Rmd index 78aa2571..ef2bb03a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -21,9 +21,11 @@ knitr::opts_chunk$set( # neuprintr The goal of *neuprintr* is to provide R client utilities for interacting with the neuPrint connectome analysis service. neuPrint is set of tools for loading and analysing connectome data into a Neo4j database. -You can find [neuprint](https://github.com/connectome-neuprint/neuPrint) on Github. There is also a great python client available from Philipp Schlegel, [neuprint-python](https://github.com/schlegelp/neuprint-python) if that's your thing. -neuPrint is currently being used for connectome analysis in aid of neuronal reconstruction efforts at Janelia Research Campus. The main focus is analysis of the [hemibrain](https://www.janelia.org/project-team/flyem/hemibrain) densely reconstructed adult Drosophila brain dataset available at https://neuprint.janelia.org/. For more information, have a look [here](https://neuprint.janelia.org/help). -Using this R package in concert with the [nat](https://github.com/jefferis/nat) ecosystem developed primarily by Greg Jefferis is highly recommended. +You can find [neuprint](https://github.com/connectome-neuprint/neuPrint) on Github. +There is also a great python client available from Philipp Schlegel, [neuprint-python](https://github.com/schlegelp/neuprint-python) if that's your thing. +neuPrint is currently being used for connectome analysis in aid of neuronal reconstruction efforts at Janelia Research Campus. The main focus is analysis of the [hemibrain](https://www.janelia.org/project-team/flyem/hemibrain), densely reconstructed adult Drosophila brain dataset available at https://neuprint.janelia.org/. +For more information, have a look [here](https://neuprint.janelia.org/help). +Using this R package in concert with the [natverse](https://github.com/natverse/natverse) ecosystem is highly recommended. ## Installation @@ -86,7 +88,7 @@ neuprint_database() neuprint_ROIs() ``` -Use the client to request data from neuprint. The \code{neuprint_fetch_custom} method will run an arbitrary cypher query against the database. For information about the neuprint data model, see the neuprint explorer web help: https://neuprint.janelia.org/help. +Use the client to request data from neuprint. The `neuprint_fetch_custom` method will run an arbitrary cypher query against the database. For information about the neuprint data model, see the neuprint explorer web help: https://neuprint.janelia.org/help. Some cyphers and other API endpoints have been explored by this package. Have a look a the functions, for example, that give you neuron skeletons, synapse locations, connectivity matrices, etc. diff --git a/README.md b/README.md index f3d9a5e4..aa6e92e1 100644 --- a/README.md +++ b/README.md @@ -1,30 +1,10 @@ -[![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.github.io) -[![Travis-CI Build -Status](https://api.travis-ci.org/natverse/neuprintr.svg?branch=master)](https://travis-ci.org/natverse/neuprintr) -[![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](http://natverse.github.io/neuprintr/reference/) - +[![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.github.io) [![Travis-CI Build Status](https://api.travis-ci.org/natverse/neuprintr.svg?branch=master)](https://travis-ci.org/natverse/neuprintr) [![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](http://natverse.github.io/neuprintr/reference/) neuprintr ========= -The goal of *neuprintr* is to provide R client utilities for interacting -with the neuPrint connectome analysis service. neuPrint is set of tools -for loading and analysing connectome data into a Neo4j database. You can -find [neuprint](https://github.com/connectome-neuprint/neuPrint) on -Github. There is also a great python client available from Philipp -Schlegel, -[neuprint-python](https://github.com/schlegelp/neuprint-python) if -that’s your thing. neuPrint is currently being used for connectome -analysis in aid of neuronal reconstruction efforts at Janelia Research -Campus. The main focus is analysis of the -[hemibrain](https://www.janelia.org/project-team/flyem/hemibrain) -densely reconstructed adult Drosophila brain dataset available at -https://neuprint.janelia.org/. -For more information, have a look -[here](https://neuprint.janelia.org/help). Using this R package in -concert with the [nat](https://github.com/jefferis/nat) ecosystem -developed primarily by Greg Jefferis is highly recommended. +The goal of *neuprintr* is to provide R client utilities for interacting with the neuPrint connectome analysis service. neuPrint is set of tools for loading and analysing connectome data into a Neo4j database. You can find [neuprint](https://github.com/connectome-neuprint/neuPrint) on Github. There is also a great python client available from Philipp Schlegel, [neuprint-python](https://github.com/schlegelp/neuprint-python) if that's your thing. neuPrint is currently being used for connectome analysis in aid of neuronal reconstruction efforts at Janelia Research Campus. The main focus is analysis of the [hemibrain](https://www.janelia.org/project-team/flyem/hemibrain), densely reconstructed adult Drosophila brain dataset available at . For more information, have a look [here](https://neuprint.janelia.org/help). Using this R package in concert with the [natverse](https://github.com/natverse/natverse) ecosystem is highly recommended. Installation ------------ @@ -41,17 +21,11 @@ library(neuprintr) Authentication -------------- -In order to use *neuprintr* you will need to be able to login to a -neuPrint server and be able to access it underlying Neo4j database. -Currently this means you have to have an authorised account. +In order to use *neuprintr* you will need to be able to login to a neuPrint server and be able to access it underlying Neo4j database. Currently this means you have to have an authorised account. -![access your bearer -token](https://raw.githubusercontent.com/natverse/neuprintr/master/inst/images/bearertoken.png) +![access your bearer token](https://raw.githubusercontent.com/natverse/neuprintr/master/inst/images/bearertoken.png) -To make life easier, you can then edit your `.Renviron` file to contain -information about the neuPrint server you want to speak with, your token -and the dataset hosted by that server, that you want to read. A -convenient way to do this is to do +To make life easier, you can then edit your `.Renviron` file to contain information about the neuPrint server you want to speak with, your token and the dataset hosted by that server, that you want to read. A convenient way to do this is to do ``` r usethis::edit_r_environ() @@ -66,20 +40,16 @@ neuprint_token="asBatEsiOIJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJlbWFpbCI6ImIsImxldmVsIjo neuprint_dataset = "hemibrain:v1.0" ``` -Make sure you have a blank line at the end of your `.Renviron` file. For -further information try about neuprintr login, see the help for -`neuprint_login()`. +Make sure you have a blank line at the end of your `.Renviron` file. For further information try about neuprintr login, see the help for `neuprint_login()`. -Finally you can also login on the command line once per session, like -so: +Finally you can also login on the command line once per session, like so: ``` r conn = neuprint_login(server= "https://neuprint.janelia.org/", token= "asBatEsiOIJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJlbWFpbCI6ImIsImxldmVsIjoicmVhZHdyaXRlIiwiaW1hZ2UtdXJsIjoiaHR0cHM7Ly9saDQuZ29vZ2xldXNlcmNvbnRlbnQuY29tLy1QeFVrTFZtbHdmcy9BQUFBQUFBQUFBDD9BQUFBQUFBQUFBQS9BQ0hpM3JleFZMeEI4Nl9FT1asb0dyMnV0QjJBcFJSZlI6MTczMjc1MjU2HH0.jhh1nMDBPl5A1HYKcszXM518NZeAhZG9jKy3hzVOWEU") ``` -This is also the approach that you would take if you were working with -more than 2 neuPrint servers. +This is also the approach that you would take if you were working with more than 2 neuPrint servers. Example ------- @@ -97,14 +67,9 @@ neuprint_database() neuprint_ROIs() ``` -Use the client to request data from neuprint. The method will run an -arbitrary cypher query against the database. For information about the -neuprint data model, see the neuprint explorer web help: -https://neuprint.janelia.org/help. +Use the client to request data from neuprint. The `neuprint_fetch_custom` method will run an arbitrary cypher query against the database. For information about the neuprint data model, see the neuprint explorer web help: . -Some cyphers and other API endpoints have been explored by this package. -Have a look a the functions, for example, that give you neuron -skeletons, synapse locations, connectivity matrices, etc. +Some cyphers and other API endpoints have been explored by this package. Have a look a the functions, for example, that give you neuron skeletons, synapse locations, connectivity matrices, etc. ``` r ?neuprint_search @@ -117,43 +82,21 @@ skeletons, synapse locations, connectivity matrices, etc. Example data ------------ -- HemiBrain (hemibrain:v1.0) : from [“A Connectome of the Adult - Drosophila Central - Brain”](https://www.biorxiv.org/content/10.1101/2020.01.21.911859v1) - (Xu, et al. 2020) +- HemiBrain (hemibrain:v1.0) : from ["A Connectome of the Adult Drosophila Central Brain"](https://www.biorxiv.org/content/10.1101/2020.01.21.911859v1) (Xu, et al. 2020) -- mushroombody (mb6) : from [“A connectome of a learning and memory - center in the adult Drosophila - brain”](https://elifesciences.org/articles/26975) (Takemura, et - al. 2017) +- mushroombody (mb6) : from ["A connectome of a learning and memory center in the adult Drosophila brain"](https://elifesciences.org/articles/26975) (Takemura, et al. 2017) -- medulla7column (fib25) : from [“Synaptic circuits and their - variations within different columns in the visual system of - Drosophila”](https://www.pnas.org/content/112/44/13711) (Takemura, - et al. 2015) +- medulla7column (fib25) : from ["Synaptic circuits and their variations within different columns in the visual system of Drosophila"](https://www.pnas.org/content/112/44/13711) (Takemura, et al. 2015) Acknowledging the data and tools -------------------------------- -neuPrint comprises a set of tools for loading and analyzing connectome -data into a Neo4j database. Analyze and explore connectome data stored -in Neo4j using the neuPrint ecosystem: -[neuPrintHTTP](https://github.com/connectome-neuprint/neuPrintHTTP), -[neuPrintExplorer](https://github.com/connectome-neuprint/neuPrintExplorer), -[Python API](https://github.com/connectome-neuprint/neuprint-python). +neuPrint comprises a set of tools for loading and analyzing connectome data into a Neo4j database. Analyze and explore connectome data stored in Neo4j using the neuPrint ecosystem: [neuPrintHTTP](https://github.com/connectome-neuprint/neuPrintHTTP), [neuPrintExplorer](https://github.com/connectome-neuprint/neuPrintExplorer), [Python API](https://github.com/connectome-neuprint/neuprint-python). -This package was created by [Alexander Shakeel -Bates](https://scholar.google.com/citations?user=BOVTiXIAAAAJ&hl=en) and -[Gregory Jefferis](https://en.wikipedia.org/wiki/Gregory_Jefferis) with -Romain -[Franconville](https://scholar.google.com/citations?user=I7yBLlsAAAAJ&hl=en) -now providing key contributions. You can cite this package as: +This package was created by [Alexander Shakeel Bates](https://scholar.google.com/citations?user=BOVTiXIAAAAJ&hl=en) and [Gregory Jefferis](https://en.wikipedia.org/wiki/Gregory_Jefferis) with Romain [Franconville](https://scholar.google.com/citations?user=I7yBLlsAAAAJ&hl=en) now providing key contributions. You can cite this package as: ``` r citation(package = "neuprintr") ``` -**Bates AS, Franconville R, Jefferis GSXE** (2019). *neuprintr: R client -utilities for interacting with the neuPrint connectome analysis -service.* **R package** version 0.4.0. -https://github.com/natverse/neuprintr +**Bates AS, Franconville R, Jefferis GSXE** (2019). *neuprintr: R client utilities for interacting with the neuPrint connectome analysis service.* **R package** version 0.4.0. diff --git a/vignettes/hemibrain_opns.Rmd b/vignettes/hemibrain_opns.Rmd index 249c0104..0b62444a 100644 --- a/vignettes/hemibrain_opns.Rmd +++ b/vignettes/hemibrain_opns.Rmd @@ -27,7 +27,8 @@ The largest draft connectome to date was released on the 22nd of January, 2020. # install if(!require('devtools')) install.packages("devtools") if(!require('natverse')) devtools::install_github("natverse/natverse") -if(!require('ComplexHeatmap')) install.packages("ComplexHeatmap") +if (!requireNamespace("BiocManager", quietly = TRUE))install.packages("BiocManager") +if(!require('ComplexHeatmap')) BiocManager::install("ComplexHeatmap") if(!require('ggnetwork')) install.packages("ggnetwork") if(!require('network')) install.packages("network")