scplotter/_pkgdown.yml at master · pwwang/scplotter · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
url: https://pwwang.github.io/scplotter/
template:
  bootstrap: 5
  light-switch: true
  bslib:
    bootswatch: litera
    pkgdown-nav-height: 80px
navbar:
  structure:
    right: [search, github]
    left: [intro, reference, articles, spatial-examples, news]
  components:
    articles:
      text: "Articles"
      menu:
        - text: "Visualizing data with LLMs"
          href: articles/Visualizing_data_with_LLMs.html
        - text: "Working with anndata (.h5ad) files"
          href: articles/Working_with_anndata_h5ad_files.html
        - text: "Knowing your spatial data and visualization"
          href: articles/Knowing_your_spatial_data_and_visualization.html
    spatial-examples:
      text: "Spatial Examples"
      menu:
        - text: "Visualizing 10x Visium data prepared with Seurat"
          href: articles/Seurat_10x_Visium.html
        - text: "Visualizing 10x VisiumHD data prepared with Seurat"
          href: articles/Seurat_10x_VisiumHD.html
        - text: "Visualizing SlideSeq data prepared with Seurat"
          href: articles/Seurat_SlideSeq.html
        - text: "Visualizing Xenium data prepared with Seurat"
          href: articles/Seurat_Xenium.html
        - text: "Visualizing Nanostring CosMx data prepared with Seurat"
          href: articles/Seurat_Nanostring_CosMx.html
        - text: "Visualizing Akoya_CODEX data prepared with Seurat"
          href: articles/Seurat_Akoya_CODEX.html
        - text: "Visualizing Visium data prepared with Giotto"
          href: articles/Giotto_Visium.html
        - text: "Visualizing VisiumHD data prepared with Giotto"
          href: articles/Giotto_VisiumHD.html
        - text: "Visualizing Xenium data prepared with Giotto"
          href: articles/Giotto_Xenium.html
        - text: "Visualizing SlideSeq data prepared with Giotto"
          href: articles/Giotto_SlideSeq.html
        - text: "Visualizing Spatial CITE-Seq data prepared with Giotto"
          href: articles/Giotto_Spatial_CITE-Seq.html
        - text: "Visualizing Nanostirng CosMx data prepared with Giotto"
          href: articles/Giotto_Nanostring_CosMx.html
        - text: "Visualizing CODEX data prepared with Giotto"
          href: articles/Giotto_CODEX.html
        - text: "Visualizing vizgen data prepared with Giotto"
          href: articles/Giotto_vizgen.html
        - text: "Visualizing seqFISH data prepared with Giotto"
          href: articles/Giotto_seqFISH.html

reference:
  - title: scRNA-seq
    desc: Functions for plotting single cell RNA-seq data
    contents:
    - CellDimPlot
    - CellStatPlot
    - CellVelocityPlot
    - FeatureStatPlot
    - ClustreePlot
    - EnrichmentPlot
    - CCCPlot
    - MarkersPlot
  - title: scTCR-seq/scBCR-seq
    desc: Functions for plotting single cell TCR-seq/BCR-seq data
    contents:
    - ClonalVolumePlot
    - ClonalAbundancePlot
    - ClonalLengthPlot
    - ClonalResidencyPlot
    - ClonalCompositionPlot
    - ClonalOverlapPlot
    - ClonalStatPlot
    - ClonalDiversityPlot
    - ClonalGeneUsagePlot
    - ClonalPositionalPlot
    - ClonalKmerPlot
    - ClonalRarefactionPlot
  - title: Spatial data visualization
    desc: Functions for plotting spatial data
    contents:
    - SpatDimPlot
    - SpatFeaturePlot
  - title: Visualizing using LLMs
    desc: Functions/Classes for visualizing using LLMs
    contents:
    - SCPlotterChat
  - title: data
    desc: Built-in data sets
    contents:
    - ifnb_sub
    - pancreas_sub
    - cellphonedb_res
  - title: Clone selectors
    desc: Functions for selecting clones
    contents:
    - shared
    - uniq
    - sel
    - top
    - eq
    - ne
    - gt
    - ge
    - lt
    - le
    - and
    - or
  - title: Re-exports
    desc: Functions that are re-exported from plotthis
    contents:
    - GSEASummaryPlot
    - GSEAPlot