_pkgdown.yml

# https://pkgdown.r-lib.org/articles/customise.html
url: https://github.com/benben-miao/TOmicsVis/
template:
  bootstrap: 5
  # bootswatch: sketchy
  theme: breeze-light
  bslib:
    code-bg: "#008888"
    code_font: {google: "JetBrains Mono"}

development:
  mode: auto

navbar:
  structure:
    left: [home, reference, articles, news, courses, omicssuite]
    right: [search, github]
  components:
    home:
      text: Home
      icon: fa-home
      href: index.html
    reference:
      text: Reference
      icon: fa-passport
      href: reference/index.html
    articles:
      text: Articles
      icon: fa-file-code
      menu:
        - text: Get Start
        - text: LongArticle
          icon: fa-weixin
          href: https://mp.weixin.qq.com/s/g8sRcK_ExlsOFniMWEJnVQ
        - text: -------
        - text: Tutorials
        - text: Tutorials
          icon: fa-file-code
          href: articles/Tutorials.html
        - text: -------
        - text: Blog
    news:
      text: Versions
      icon: fa-code-branch
      href: news/index.html
    courses:
      text: Courses
      icon: fa-film
      menu:
        - text: Platforms
        - text: BiliBili
          icon: fa-youtube
          href: https://space.bilibili.com/34105515/channel/series
        - text: WeChat
          icon: fa-weixin
          href: https://mp.weixin.qq.com/s/mVXJmHPAnC9J1-zMj7eG7g
    omicssuite:
      text: OmicsSuite
      icon: fa-dna
      href: https://github.com/OmicsSuite/

home:
  links:
  - text: OmicsSuite
    href: https://github.com/OmicsSuite/
  - text: OmicsSuite website
    href: https://github.com/OmicsSuite/OmicsSuite.github.io

reference:
- title: TOmicsVis Shinyapp
  contents:
  - tomicsvis

- title: ①Samples Statistics
  desc: Statistical sample outliers, correlation among samples, distance among samples, etc.
  contents:
  - quantile_plot
  - box_plot
  - violin_plot
  - survival_plot

- title: ②Traits Analysis
  desc: Statistical analysis of traits, such as adding R and P values to box plots and violin plots, and more dimensionality reduction analysis.
  contents:
  - corr_heatmap
  - pca_analysis
  - pca_plot
  - tsne_analysis
  - tsne_plot
  - umap_analysis
  - umap_plot
  - dendro_plot

- title: ③Differential Expression Analyais
  desc: Analysis and visualization based on gene expression data and differentially expressed genes.
  contents:
  - venn_plot
  - upsetr_plot
  - flower_plot
  - volcano_plot
  - ma_plot
  - heatmap_group
  - circos_heatmap
  - chord_plot

- title: ④Advanced Analysis
  desc: Advanced analysis of Transcriptome includes exploring gene expression trends of multiple groups of samples, constructing co expression modules for genes, and exploring genes related to traits in expression modules.
  contents:
  - gene_rank_plot
  - gene_cluster_trend
  - trend_plot
  - wgcna_pipeline
  - network_plot
  - heatmap_cluster

- title: ⑤GO and KEGG Enrichment
  desc: GO and KEGG enrichment analysis and visualization.
  contents:
  - go_enrich
  - go_enrich_stat
  - go_enrich_bar
  - go_enrich_dot
  - go_enrich_net
  - kegg_enrich
  - kegg_enrich_bar
  - kegg_enrich_dot
  - kegg_enrich_net

- title: ⑥Tables Operations
  desc: Quickly manipulate specific Transcriptome data structures.
  contents:
  - table_split
  - table_merge
  - table_filter
  - table_cross

- title: Example datasets in TOmicsVis
  desc: Example datasets in TOmicsVis.
  contents:
  - weight_sex
  - traits_sex
  - survival_data
  - gene_expression
  - gene_expression2
  - gene_expression3
  - samples_groups
  - degs_lists
  - degs_stats
  - degs_stats2
  - network_data
  - gene_go_kegg
  - gene_go_kegg2