jefferislab/lhns

A repository for neuron data related to the fly lateral horn

lhns's Issues

process_lhn_name returns anatomy.group NANA for NA input

> lhns::process_lhn_name(c("AV2d1", NA))
   pnt anatomy.group cell.type
1  AV2          AV2d     AV2d1
2 <NA>          NANA      <NA>

Alternative to git lfs based distribution

As discussed we need to settle on a better distribution mode for the content of this package. I think there are few basic options:

1. Use regular neuronlist objects, but construct them at package build or package load from separately versioned objects that contain the metadata and the neurons. This can still result in package bloat if the object containing the neurons is repeatedly resaved for any reason, but it should reduce this substantially.
2. Use neuronlistfh objects storing the data within the package. I have not tried this previously (there may be a path issue based on the location of this data since it would not be possible to provide an absolute path to the location of the individual neurons).
3. Use neuronlistfh but store the objects remotely. This is what we did for the NBLAST paper. It works, there is versioning of the data objects (because the md5 hashes are embedded within the neuronlistfh object) but it doesn't guarantee that the neuron data are actually there – the user needs to explicitly request the download and it can be a little slow.
4. As one last alternative, could consider something a bit like 3, but putting a monolithic data object on zenodo. This would probably result in faster downloads and the objects would be versioned. This would require new code to support the upload/download from zenodo.

fru-M-100206 is badly misregistered

> plot3d("fru-M-100206",db=most.lhns, soma=T)
> plot3d(FCWB)

Missing PNT for AD1b2 cell 120714c4

               id  sex LH_side  pnt anatomy.group cell.type coreLH good.trace dendritic.cable.in.lh dendritic.cable type
120714c4 120714c4 <NA>    <NA> <NA>          AD1b     AD1b2   TRUE       TRUE                    NA              NA   ON
140612c0 140612c0 <NA>    <NA>  AD1          AD1b     AD1b2   TRUE       TRUE                    NA              NA   ON
140616c0 140616c0 <NA>    <NA>  AD1          AD1b     AD1b2   TRUE       TRUE                    NA              NA   ON

Installation typo?

https://github.com/jefferislab/lhns/blob/master/README.md#installation

devtools::install("jefferislab/lhns")

should it be install_github?

Document lh.mcfo

lh.mcfo still not documented – this is the last warning for the package.