NEWS.md

In natverse/flycircuit: Functions to support the analysis of the FlyCircuit single neuron dataset

flycircuit 0.6.9

• new functions fc_read_neurons() to read traced skeletons from the flycircuit website, fc_get_ids() to get a list of neuron identifiers, fc_page() to see the details page for a neuron (#44) (thanks to @alexanderbates)
• Fix FCWBNP.surf by updating to nat.flybrains version (#43)
• switch to natverse github organisation

flycircuit 0.6.8

• Ensure that flycircuit package can be installed from github with development versions of all its dependencies (fixes to github remotes etc). This was as a result of difficulties installing on the VFB opencpu docker instance.
• dev: fixes to travis build configuration (switch to non sudo trusty dist)

flycircuit 0.6.7

• Update annotation database (1 August 2016, now 7021 NeuronType annotations)

flycircuit 0.6.6

• Add fc_neuron_type
• Add online docs with pkgdown
• Insist on nat >= 1.8.8

flycircuit 0.6.5

• update annotation database (1 April 2015, now 6565 NeuronType annotations)
• add fc_glom function to find antennal lobe glomeruli for fc neurons
• dev: update to roxygen2 v4.1.1

flycircuit 0.6.4

• update annotation database

flycircuit 0.6.3

• load_si_data works with bigmat pairs of the form x.desc+x.bin
• load_si_data no longer attempts to check for object existence
• doc: load_si_data improvements
• dev: fix check errors

flycircuit 0.6.2

• depend on nat

flycircuit 0.6.1

• fix bug when creating data directories (based on rappdirs location) on a new system

flycircuit 0.6

• Store persistent data in directory determined by rappdirs package
• add load_si_data
• add plot3d.APResult
• Add apclusterfc
• fc_download_data (always) returns path to file
• ... and can use local file (with warning) if remote url unreadable
• ... plus additional bug fixes
• add as.data.frame.APResult for affinity propagation clustering results
• fc_nblast normalises like sub_score_mat

flycircuit 0.5.3

• add fc_sex utility function to find sex of animal for any valid flycircuit neuron identifier.
• give hclustfc an unsquare argument

flycircuit 0.5.2

• fix subtle bug in plot3dfc revealed only when this is used inside a function.
• plot3dfc can now accept a character vector for the db argument.

flycircuit 0.5.1

• fix hclustfc (was not attaching scoremat)
• refactor fc_subscoremat (using nat.nblast::sub_score_mat)
• dev: remove internal diagonal function and tests

flycircuit 0.5

• deprecated pop3dfc in favour of nat::npop3d
• refactored plot3dfc to use nat::plot3d.character. plot3dfc will be deprecated in favour of plot3d.character when that function can coped with multiple identifier styles.

flycircuit 0.4.1

• extensive refactoring so that fc_nblast, hclustfc and friends are now thin wrappers on more generic functions in nat.nblast
• plot3dfc can handle NA soma positions
• update annotation table
• docs: plot3dfc improvements
• add fcgn_forfile

flycircuit 0.3.1

• significant (20x in my tests) speedup for hclustfc using large ff objects containing raw scores.

flycircuit 0.3

• ready for use by external code
• add subset.hclust, plot3d.hclust
• make sure that clustering based on pre-computed nblast scores all works properly and that ff cached versions of the data are available
• only provide ff cached versions of raw scores for download and normalise on the fly
• fix errors in package vignette

natverse/flycircuit documentation built on Jan. 26, 2023, 6:46 p.m.