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R package flycircuit

Home Page: https://natverse.github.io/flycircuit

License: GNU General Public License v3.0

R 96.18% TeX 3.82%

drosophila natverse neuroanatomy neuroanatomy-toolbox r

flycircuit's Introduction

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#>   as.mesh3d.ashape3d rgl
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#> Loading required package: nat.flybrains
#> Loading required package: nat.templatebrains
#> Loading required package: nat.nblast
# example 3D plot of some neurons
plot(kcs20, col=type)

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#> package         remote         local          source   repo                        status 
#> --------------  -------------  -------------  -------  --------------------------  -------
#> bit64           0.9-7.1        0.9-7          CRAN     https://cran.rstudio.com/   x      
#> data.table      1.13.0         1.12.8         CRAN     https://cran.rstudio.com/   x      
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#> xfun            0.16           0.15           CRAN     https://cran.rstudio.com/   x      
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flycircuit's People

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c00cjz00 donquixotedonflamingo

flycircuit's Issues

support FlyCircuit 1.2

Essental:

support for FlyCircuit 1.2 ids (probably keeping track of which release contained which ids)
remove all use of gene_name or idid as an id (these both seem to have been retired)
update flycircuit-ids documentation accordingly to better explain the mess

Desirable:

map to canonical side
process for NBLAST

Hopefully:

package SWC data in FCWB space
figure out annotations for new neurons (at least those that match existing annotations)
complete annotation in conjunction with EM data?

load_si_data should have update=FALSE by default

Otherwise why bother caching all the date?!

fc_download_data should check local disk for data more intelligently

It would be best if it used e.g. url header to decide whether an update was required

diagonal function should check diag attribute

see #13

hclustfc docs should refer to nhclust

load_si_data fails on Windows

another case of not setting binary mode

> sc=fc_nblast("fru-M-200266")
attaching: allbyallblastcv4.5
Error in readRDS(fffile) : error reading from connection

hclustfc fails because scorematrix is not attached

glom=="VAsomething" in allpndps.rds is VA4?

I wrote a short script, which NBLASTed 2 Flycircuit PNs (glom=="VAsomething") against FAFB PNs of VAs glomeruli, to see which VA glomerulus they are from. You should be able to just run the script and it will print the result.

Looks like they are VA4. When plotted, they look like VA4 as well.

add diagonal to existing score matrix objects

could just be an attribute in the ff.rds object

load_si_data object check is broken

The function definition looks like this:

load_si_data <- function(data_name, type=c('auto', 'data', 'db', 'bigmat', 'ff', 'plain'), overwrite=FALSE, ...) {
  if(!exists(data_name, where=.GlobalEnv)) {
  # ...
  # code that loads the data 
  }
}

but in fact data_name is almost always not the same as the object that is loaded. I therefore think that it would be best to drop the pretence of an existence check for the object. What do you think @ajdm?

load_si_data fails for some bigmat pairs

Specifically it assumes that the data file does not have a file extensions, whereas .bin is common.

load_fcdata can blast pre-existing objects

Currently, load_fcdata() returns NULL if the data is already loaded. This can cause objects to be blasted away by doing:

foo <- load_fcdata('foo')
# some other code
foo <- load_fcdata('foo')

Would it not be better to return the existing object instead?

fc_download_data can block fetching header

looks like this is some strange interaction with the httr::HEAD/curl. We have seen serveral cases where HEAD blocks repeatedly, but curl -I on the commandline works fine.

One option would be switch to RCurl if that does something different.

fc_gene_name and friends should have an ignore.case=TRUE options

This would would ignore capitalisation errors by converting all ids to e.g. upper case.

Add example for apclusterfc

Give hclustfc an unsquare argument

Since for plotting we would rather use the distance not distance^2 as reported by hclust.

add apclusterfc

Extend fc_neuron_type function

Could this function look up both annotation_class "NeuronType" (currently) and "ALGlomerulus"?

merge functionality of plot3dfc / plot3d.character / plot3d.neuronlist

add smat score matrix

there are two of these, one combining the alpha value (ratio of first eigenvalue total IIRC) of the two dot products, one using unit vectors in both cases (the default)

plot3dfc should not try to plot neurons that don't exist in db

Because if the db is a neuronlstfh object one gets cryptic error messages like:

Error in get(i, envir = hm) : object 'DvGlutMARCM-F132_seg1' not found

if the neuron does not exist.

fc_attach_ff/bigmat should normalise paths

ff is not happy with paths containing a ~

fc_nblast can be very slow

primarily due to reverse scores. But for some reason it seems to me that this can be much worse than using bigmat,

I just had an example with rstudio where it took a minute to do 1 x 3677 normalised scores. My suspicion is that it was actually some unrelated problem e.g. GUI update that was interleaved. These kind of error messages are typical when changing location with an X session in progress:

Tue Mar 18 14:32:29 mac1041-14.lmb.internal rsession[355] <Error>: kCGErrorIllegalArgument: CGSGetDisplayBounds (display 3f003d)

However, there is a still a more general speed issue to be tracked down since I have seen a behaviour where attaching an ff matrix to the global environment can bring access speed benefits.