Merge branch 'master' of github.com:jefferislab/neuprintr

* 'master' of github.com:jefferislab/neuprintr:
  Updated intro
  Update hemibrain_opns.Rmd

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.
 

README.md

@@ -1,30 +1,10 @@
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-[![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/)
-<img src="man/figures/logo.svg" align="right" height="139" />
+[![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/) <img src="man/figures/logo.svg" align="right" height="139" />
 
 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
-<a href="https://neuprint.janelia.org/" class="uri">https://neuprint.janelia.org/</a>.
-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 <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
 ------------
@@ -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:
-<a href="https://neuprint.janelia.org/help" class="uri">https://neuprint.janelia.org/help</a>.
+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.
+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.
-<a href="https://github.com/natverse/neuprintr" class="uri">https://github.com/natverse/neuprintr</a>
+**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>

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")