vfbconnectr's Introduction

vfbconnectr

vfbconnectr provides a simple R wrapper (via reticulate) for the VFB_connect Python library that enables programmatic access to the https://virtualflybrain.org website and associated services. VFB_connect is developed by the core VFB team.

Installation

remotes::install_github("natverse/vfbconnectr")

vfbconnectr relies on the reticulate package and a Python installation. To learn more about how reticulate is used within R packages, see this article. We use the automatic configuration method. In theory this should offer to install any necessary python dependencies into a r-reticulate python environment.

Example

This is the R equivalent of the basic examples for the Python library. Essentially convert . to $ and turn ['text'] into list("text") and you should be good to go.

library(vfbconnectr)
## basic example code

vc=VfbConnect()

vc$neo_query_wrapper$get_type_TermInfo(list('FBbt_00003686'))

vc$neo_query_wrapper$get_DataSet_TermInfo(list('Ito2013'))

vc$neo_query_wrapper$get_anatomical_individual_TermInfo(list('VFB_00010001'))
# Get all terms relevant to a brain region (all parts and all overlapping cells$
# Query by label supported by default$
vc$get_terms_by_region('fan-shaped body')

The VFB_connect python library has a full documentation site at https://vfb-connect.readthedocs.io/.

Next steps

make a general R helper function to improve formatting of results
wrap some functions in R functions to improve formatting of results and avoid any need to worry about whether inputs must be in a list or not.
more examples ...

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