_pkgdown.yml

url: https://natverse.org/nat.nblast/
template:
  bootstrap: 5
navbar:
  structure:
    left:
    - home
    - intro
    - reference
    - articles
    - tutorials
    - news
    - help
    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: NBLAST Clustering
        href: articles/NBLAST-Clustering.html
    news:
      text: Changelog
      href: news/index.html
    natverse:
      text: natverse
      href: https://natverse.github.io
    github:
      icon: fa-github fa-lg
      href: https://github.com/natverse/nat.nblast
    help:
      text: Help
      href: SUPPORT.html
reference:
- title: Package Overview
  desc: Provides an overview of key functions and classes
  contents: nat.nblast-package
- title: Key functions
  desc: The main entry points to neuron search and clustering
  contents:
  - nblast
  - nblast_allbyall
  - nhclust
- title: Plotting results
  desc: Visualise pairwise neuron search or clustering results
  contents:
  - plot3d.hclust
  - show_similarity
  - subset.hclust
- title: Scoring Matrices
  desc: Calculate the scoring matrices that define NBLAST similarity
  contents:
  - create_scoringmatrix
  - calc_score_matrix
  - calc_prob_mat
  - calc_dists_dotprods
  - smat.fcwb
- title: Mid level functions for result matrices
  desc: |
    Functions that you might use to manipulate matrices containing all by all NBLAST results for use with other clustering strategies (besides nhclust)
  contents:
  - sub_score_mat
  - sub_dist_mat
  - sparse_score_mat
- title: Low level search functions
  desc: Intended for developer use
  contents:
  - NeuriteBlast
  - neuron_pairs
  - WeightedNNBasedLinesetMatching
  - fctraces20
- title: Matrix utility functions
  desc: Intended for developer use
  contents:
  - diagonal
  - '['
  - fill_in_sparse_score_mat
  - fill_pairs_sparse_score_mat