_pkgdown.yml

navbar:
  type: default
  left:
  - icon: fa-home fa-lg
    href: index.html
  - text: Reference
    href: reference/index.html
  - text: Articles
    menu:
    - text: "Introduction to neurons and neuronlists"
      href: articles/neurons-intro.html
    - text: "Working with individual neurons as graph structures"
      href: articles/neurons-as-graph.html
    - text: "NeuroGeometry: Analysing 3D morphology of neurons"
      href: articles/NeuroGeometry.html
  - text: News
    href: news/index.html
  - text: Installation
    href: articles/Installation.html
  - text: Learn
    href: index.html#learn
  - text: Help
    href: index.html#help
  right:
  - icon: fa-github fa-lg
    href: https://github.com/jefferis/nat

articles:
- title: All vignettes
  desc: ~
  contents:
  - '`Installation`'
  - '`neurons-intro`'
  - '`neurons-as-graph`'
  - '`NeuroGeometry`'
reference:
  - title: Package Help
    desc: Provides an overview of key functions and classes
    contents:
    - "`nat-package`"
  - title: Neurons (traced)
    desc: Functions for working with traced neurons (fully connected tree structures)
    contents:
    - neuron
    - read.neuron
    - write.neuron
    - plot.neuron
    - subset.neuron
    - prune
    - prune_vertices
    - Ops.neuron
    - scale.neuron
    - resample
    - smooth_neuron
    - potential_synapses
    - normalise_swc
  - title: Neurons (as graphs)
    desc: Functions for working with the graph structure of neurons
    contents:
    - ngraph
    - graph.nodes
    - prune_strahler
    - rootpoints
    - seglengths
    - seglist
    - seglist2swc
    - segmentgraph
    - spine
    - strahler_order
  - title: Skeletonised Neurons (dotprops aka vector cloud)
    desc: Functions for working with skeletonised neurons consisting of 
      unconnected vectors rather than a fully connected tree.
    contents:
    - dotprops
    - subset.dotprops
    - Ops.dotprops
  - title: Collections of Neurons (neuronlists)
    desc: Functions for working with collections of neurons, which are packaged as 
      neuronlist objects with an attached data.frame containing metadata.
    contents:
      - neuronlist
      - read.neurons
      - write.neurons
      - nlapply
      - plot.neuronlist
      - plot3d.neuronlist
      - subset.neuronlist
      - summary.neuronlist
      - as.neuronlist
      - c.neuronlist
      - as.data.frame.neuronlist
      - is.neuronlist
      - "`*.neuronlist`"
      - "`neuronlist-dataframe-methods`"
  - title: Collections of Neurons with Remote Data (neuronlistfh)
    desc: Functions for working with collections of neurons where the data will be
      dynamically loaded into memory from disk and/or downloaded from a remote site.
    contents: 
      - neuronlistfh
      - read.neuronlistfh
      - write.neuronlistfh
      - remotesync
      - as.neuronlist.neuronlistfh
      - "`[.neuronlistfh`"
  - title: Surfaces and Landmarks (hxsurf, mesh3d)
    desc: Functions for working with surface data, either in a class hxsurf 
      modeled on Amira's representation of surfaces or the rgl::mesh3d class.
    contents:
      - read.hxsurf
      - write.hxsurf
      - read.landmarks
      - plot3d.hxsurf
      - subset.hxsurf
      - as.hxsurf
      - as.mesh3d
      - pointsinside
  - title: 3D Plotting of objects
    desc: Functions to help plot neurons and surfaces in 3D and to review and 
      identify objects by interactive selection.
    contents:
      - plot3d
      - nopen3d
      - nview3d
      - npop3d
      - pan3d
      - find.neuron
      - find.soma
      - nlscan
      - plot3d.boundingbox
      - plot3d.dotprops
      - plot3d.hxsurf
      - plot3d.neuron
      - plot3d.cmtkreg
  - title: 3D Geometry
    desc: Functions for analysing 3D geometry of neurons and other objects
    contents:
    - nvertices
    - xyzmatrix
    - plane_coefficients
    - intersect_plane
  - title: Object transformation
    desc: Generic strategies for transforming 3D objects/images
    contents:
    - xform
    - mirror
    - reglist
    - xformimage
    - xformpoints
    - simplify_reglist  
  - title: Images (im3d)
    desc: Functions for working with 3d image volumes 
    contents:
    - im3d
    - "`im3d-io`"
    - as.im3d
    - is.im3d
    - imslice
    - image.im3d
    - imscalebar
    - flip
    - projection
    - threshold
    - mask
    - unmask
    - clampmax
    - boundingbox
    - makeboundingbox
    - origin
    - voxdims
    - nrrd.voxdims
    - "`im3d-coords`"
    - coord2ind
    - ind2coord
    - sub2ind
    - imexpand.grid
    - materials
  - title: CMTK Registration
    desc: Functions to interface to the CMTK image registration suite
    contents:
    - cmtk.bindir
    - cmtk.version
    - cmtkparams2affmat
    - affmat2cmtkparams
    - cmtk.dof2mat
    - cmtk.mat2dof
    - cmtk.extract_affine
    - cmtk.reformatx
    - cmtk.statistics
    - cmtk.targetvolume
    - cmtkreg
    - cmtkreglist
    - cmtk.call
  - title: Sample Data
    desc: Sample data objects (neurons, surfaces)
    contents:
      - Cell07PNs
      - kcs20
      - MBL.surf
  - title: Generic Functions
    desc: Generic versions of base functions for which we provide specialised 
      methods for nat objects.
    contents:
    - intersect
    - setdiff
    - subset
    - union
  - title: Utility Functions
    desc: Functions primarily intended for developer use
    contents:
    - ndigest
    - all.equal.dotprops
    - all.equal.im3d
    - all.equal.neuron
  - title: File formats
    desc: Support for different formats. It is generally recommended to use more
      generic functions such as read.neuron(s) rather than these functions.
    contents:
    - fileformats
    - read.cmtk
    - read.cmtkreg
    - read.morphml
    - read.neuron.fiji
    - read.neuron.neuroml
    - read.neuron.swc
    - read.nrrd
    - read.vaa3draw
    - read.amiramesh
    - write.amiramesh
    - write.cmtk
    - write.cmtkreg
    - write.nrrd
    - write.vtk
    - amiratype  
    - is.amiramesh
    - is.fijitraces
    - is.neuroml
    - is.nrrd
    - is.swc
    - is.vaa3draw