_pkgdown.yml

toc:
  depth: 3
navbar:
  structure:
    left:
    - home
    - intro
    - reference
    - articles
    - install
    - learn
    - help
    - news
    right: 
    - natverse
    - github
  components:
    home:
      icon: fa-home fa-lg
      href: index.html
    reference:
      text: Reference
      href: reference/index.html
    articles:
      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: 3D graphics
        href: articles/plotly.html
      - text: 'NeuroGeometry: Analysing 3D morphology of neurons'
        href: articles/NeuroGeometry.html
    news:
      text: Changelog
      href: news/index.html
    install:
      text: Installation
      href: articles/Installation.html
    learn:
      text: Learn
      href: index.html#learn
    help:
      text: Help
      href: index.html#help
  right:
    natverse:
      text: natverse
      href: https://natverse.github.io
    github:
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      href: https://github.com/natverse/nat
articles:
- title: All vignettes
  desc: ~
  contents:
  - '`Installation`'
  - '`neurons-intro`'
  - '`neurons-as-graph`'
  - '`NeuroGeometry`'
  - '`plotly`'
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
    - prune_in_volume
    - Ops.neuron
    - scale.neuron
    - resample
    - seglist
    - seglist2swc
    - seglengths
    - smooth_neuron
    - normalise_swc
  - title: Neurons (as graphs)
    desc: Functions for working with the graph structure of neurons
    contents:
    - ngraph
    - graph.nodes
    - rootpoints
    - segmentgraph
    - distal_to
    - spine
    - strahler_order
    - prune_strahler
    - get_topo_features
    - prune_twigs
    - simplify_neuron
    - stitch_neuron
    - stitch_neurons
    - stitch_neurons_mst
    - reroot
  - 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
      - neuronlistz
      - 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
      - c.hxsurf
      - as.mesh3d
      - pointsinside
  - title: 3D Plotting of Objects
    desc: Functions to help plot neurons, surfaces and other 3D objects via RGL.
    contents:
      - plot3d
      - nopen3d
      - nclear3d
      - nview3d
      - npop3d
      - pan3d
      - wire3d
      - nlscan
      - plot3d.boundingbox
      - plot3d.dotprops
      - plot3d.hxsurf
      - plot3d.neuron
      - plot3d.cmtkreg
      - plot3d.ngraph
  - title: 3D Interaction with Objects
    desc: Functions to review, identify, and modify objects by interactive selection in RGL windows.
    contents:
      - find.neuron
      - find.soma
      - select_points
      - correct_root
      - prune_online
      - make_model
  - title: 3D Geometry
    desc: Functions for analysing 3D geometry of neurons and other objects
    contents:
    - nvertices
    - xyzmatrix
    - potential_synapses
    - overlap_score
    - sholl_analysis
    - plane_coefficients
    - intersect_plane
  - title: Object transformation
    desc: Generic strategies for transforming 3D objects/images and registration
    contents:
    - xform
    - mirror
    - reglist
    - xformimage
    - xformpoints
    - simplify_reglist  
    - tpsreg
  - 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
      - dl1neuron
      - 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