Package Help

Provides an overview of key functions and classes

flycircuit-package

Support functions for analysis of raw image data provided by flycircuit.tw

Identifiers and Annotations

There are at least 3 different kinds of identifiers in use with the flycircuit database. These functions convert between them as well as making additional metadata available. Furthermore annotations carried out in the course of the Costa et al. NBLAST study are also available - these include the identification of 5400 neuronal types as well as the glomeruli innervated by 433 olfactory projection neurons.

annotation

A dataframe containing manual annotations of some FlyCircuit neurons

fc_glom()

Antennal lobe glomerulus (where applicable) for FlyCircuit identifiers

fc_neuron_type() fc_annotated_class()

Return metadata including NeuronType for FlyCircuit neurons

fc_sex()

return sex of the animal for one or more FlyCircuit identifiers

fcidtable

fcidtable - Data.frame of flycircuit identifiers

fc_gene_name() fc_idid() fc_neuron()

Convert between different FlyCircuit identifiers

fcgn_forfile()

Return the flycircuit gene_name identifier for a file

fc_get_ids()

Scrape FlyCircuit.tw for neuron IDs

Read neuron skeletons / web data

See the package README for other data download options.

fc_read_neurons()

Fetch FlyCircuit neuron skeletons from the Taiwan FlyCircuit server

fc_page()

See a FlyCircuit neuron on the FlyCircuit website

Clustering and searching

apclusterfc()

Affinity propagation clustering of FlyCircuit neurons

as.data.frame(<APResult>)

Convert APResult (apcluster output) to dataframe

fc_nblast()

Return (normalised) nblast similarity scores for FlyCircuit neurons

hclustfc()

Cluster a set of FlyCircuit neurons identified by gene_name

fc_subscoremat()

Return scores (or distances) for given query and target neurons

kcs20scores

A matrix containing all by all nblast similarity scores for 20 neurons

Plotting and surfaces

FCWB.surf

FCWB.surf - Surface model of FCWB FlyCircuit reference brain

FCWBNP.surf

FCWBNP.surf - Surface model of FlyLight neuropil segmentation in FlyCircuit coordinate space

fcwbnpsurf()

Plot 3D surfaces of the FlyLight neuropil segmentation in FlyCircuit coordinate space

fcwbsurf()

Plot a 3D surface of the FlyCircuit reference brain

getRegionsFromSurf()

Return a list of regions contained in a surface

getRegionSurf()

Creates a new surface containing specified regions from a given surface

plot3d(<APResult>)

Plot exemplar neurons/all cluster members after clustering by affinity propagation

plot3dfc()

Plot FlyCircuit neurons using rgl

pop3dfc()

Remove plotted FlyCircuit neurons (deprecated, see nat::npop3d)

selectRegionsFromSurf()

Select regions from a surface

dpscan()

Scan through a set of flycircuit neurons

drawRegionSurf()

Draw surface corresponding to a given list of regions from surface object

Support for remote / optional data

Some flycircuit functionality depends on data which is not bundled into the R package (since it is about 4GB in size). These functions handle download and access to such data.

download.file.wcheck()

Download a remote file if it is new or updated

fc_attach_bigmat()

Attach a big.matrix (typically used for all-by-all blast distances)

fc_attach_ff()

Attach an ff object (typically used for all-by-all blast distances)

fc_download_data()

Download a data file from a remote location

load_fcdata()

Load an rda/rds object cached on disk into the Global Environment

load_fcdb()

Load a database cached in the db subfolder into the Global Environment

load_si_data()

Load NBLAST supplemental data objects, downloading when required