search

natverse / neuprintr

R client utilities for interacting with the neuPrint connectome analysis service
http://natverse.org/neuprintr
3 stars 3 forks source link

neuprint_common_connectivity broken #67

Open romainFr opened 4 years ago

romainFr commented 4 years ago

Fails with 

Error in names(x) <- paste("V", seq_along(x), sep = "") : 
  'names' attribute [1] must be the same length as the vector [0]
jefferis commented 4 years ago

Can you give an example? Is it for any input?

Sent from my iPhone

On 3 Feb 2020, at 19:38, Romain Franconville notifications@github.com wrote:

Fails with

Error in names(x) <- paste("V", seq_along(x), sep = "") : 'names' attribute [1] must be the same length as the vector [0] — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

jefferis commented 4 years ago

@romainFr is this related to change of dataset to hemibrain:v1.0.1?

romainFr commented 4 years ago

My mistake, it is actually working. I got confused because it only returns partners common to all inputed neurons and I was looking for partners common to some (at least two) of the inputed neurons.

mmc46 commented 4 years ago

Sorry to maybe reopen, but then this

it only returns partners common to all inputed neurons and I was looking for partners common to some (at least two) of the inputed neurons.

is different behaviour to neuPrint Explorer, where common partners to a subset of bodyids are returned. Example bodyids: 1734350788,1734350908,1765040289,5813039315,722817260

Just wanted to double check it is correct.

romainFr commented 4 years ago

Actually for me now neuprint explorer returns all the partners of all the neurons (whether any of those partners are in common or not), which is not super useful. Maybe we could have an ALL/ANY option in neuprintr_common_connectivity to switch between different behaviors?

alexanderbates commented 4 years ago

I don't really use this function very much, nor am I sure that others in our group do. So feel free to update it to work sensibly. The behaviour does not need to be the same a neuPrint explorer, if whatever we go with is more useful and well documented.

jefferis commented 4 years ago

I also agree that requiring partners to have connections to all the query neurons is not the behaviour I would expect. However more importantly, the prepost argument again seems to be backwards. i.e. you specify pre and you get the outputs.