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mkdocs.yml
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site_name: scimap
site_description: Single-Cell Image Analysis Package
site_author: Ajit Johnson Nirmal
repo_url: https://github.com/ajitjohnson/scimap
edit_uri: https://github.com/ajitjohnson/scimap/edit/master/docs
# mkdocs.yml
theme:
name: "material"
logo: ./assets/favicon.png
favicon: ./assets/favicon.png
features:
- navigation.instant
features:
- navigation.tabs
- navigation.tabs.sticky
- navigation.top
- search.highlight
palette:
- scheme: default
primary: white
toggle:
primary: white
icon: material/toggle-switch-off-outline
name: Switch to dark mode
- scheme: slate
primary: white
toggle:
icon: material/toggle-switch
name: Switch to light mode
nav:
- Home: 'index.md'
- Install: 'Getting Started.md'
- Index: 'Tools Shortcut.md'
- Functions:
- Pre Processing:
- mcmicro_to_scimap: 'Functions/pp/mcmicro_to_scimap.md'
- log1p: 'Functions/pp/log1p.md'
- rescale: 'Functions/pp/rescale.md'
- combat: 'Functions/pp/combat.md'
- Tools:
- phenotype_cells: 'Functions/tl/phenotype_cells.md'
- cluster: 'Functions/tl/cluster.md'
- umap: 'Functions/tl/umap.md'
- foldchange: 'Functions/tl/foldchange.md'
- spatial_distance: 'Functions/tl/spatial_distance.md'
- spatial_interaction: 'Functions/tl/spatial_interaction.md'
- spatial_count: 'Functions/tl/spatial_count.md'
- spatial_lda: 'Functions/tl/spatial_lda.md'
- spatial_expression: 'Functions/tl/spatial_expression.md'
- spatial_cluster: 'Functions/tl/spatial_cluster.md'
- spatial_pscore: 'Functions/tl/spatial_pscore.md'
- spatial_aggregate: 'Functions/tl/spatial_aggregate.md'
- spatial_similarity_search: 'Functions/tl/spatial_similarity_search.md'
- Plotting Functions:
- image_viewer: 'Functions/pl/image_viewer.md'
- addROI_image: 'Functions/pl/addROI_image.md'
- gate_finder: 'Functions/pl/gate_finder.md'
- napariGater: 'Functions/pl/napariGater.md'
- heatmap: 'Functions/pl/heatmap.md'
- markerCorrelation: 'Functions/pl/markerCorrelation.md'
- groupCorrelation: 'Functions/pl/groupCorrelation.md'
- distPlot: 'Functions/pl/distPlot.md'
- densityPlot2D: 'Functions/pl/densityPlot2D.md'
- cluster_plots: 'Functions/pl/cluster_plots.md'
- umap: 'Functions/pl/umap.md'
- foldchange: 'Functions/pl/foldchange.md'
- spatial_scatterPlot: 'Functions/pl/spatial_scatterPlot.md'
- spatial_distance: 'Functions/pl/spatial_distance.md'
- spatial_interaction: 'Functions/pl/spatial_interaction.md'
- spatialInteractionNetwork: 'Functions/pl/spatialInteractionNetwork.md'
- spatial_pscore: 'Functions/pl/spatial_pscore.md'
- stacked_barplot: 'Functions/pl/stacked_barplot.md'
- pie: 'Functions/pl/pie.md'
- voronoi: 'Functions/pl/voronoi.md'
- Helper Functions:
- classify: 'Functions/hl/classify.md'
- rename: 'Functions/hl/rename.md'
- addROI_omero: 'Functions/hl/addROI_omero.md'
- dropFeatures: 'Functions/hl/dropFeatures.md'
- merge_adata_obs: 'Functions/hl/merge_adata_obs.md'
- animate: 'Functions/hl/animate.md'
- scimap_to_csv: 'Functions/hl/scimap_to_csv.md'
- Tutorials:
- Index: 'tutorials/md/spatial_biology_scimap.md'
- Setup:
- Install Scimap: 'tutorials/md/install_scimap.md'
- Demo Data: 'tutorials/md/demo_data_scimap.md'
- Prepare Demo: 'tutorials/md/anndata_scimap.md'
- Cell Phenotyping:
- Unsupervised clustering: 'tutorials/md/clustering_scimap.md'
- Prior knowledge driven: 'tutorials/md/scimap_phenotyping.md'
- Add ROIs: 'tutorials/md/add_rois_scimap.md'
- Explore cell types: 'tutorials/md/cell_proportion_scimap.md'
- Spatial Analysis:
- Distance measurement: 'tutorials/md/spatial_analysis_scimap.md'
- Interaction analysis: 'tutorials/md/cell_interaction_scimap.md'
- Proximity scores: 'tutorials/md/proximity_scimap.md'
- Search patterns: 'tutorials/md/spatial_search_scimap.md'
- Cellular Neighbourhoods:
- Spatial LDA: 'tutorials/md/spatial_lda_scimap.md'
- Spatial Lag: 'tutorials/md/spatial_lag_scimap.md'
- Helper:
- Export data: 'tutorials/md/export_scimap.md'
- Animate: 'tutorials/md/animate_scimap.md'
- Other helpers: 'tutorials/md/scimap_helper_functions.md'
- Videos: 'tutorials/md/scimap_video.md'
- Archive:
- Getting Started with Scimap: 'tutorials/archive/1-scimap-tutorial-getting-started.md'
- Cell-Phenotyping using Scimap: 'tutorials/archive/2-scimap-tutorial-cell-phenotyping.md'
- Cell-Phenotyping and adding ROIs: 'tutorials/archive/3-Cell_Type_calling_and_adding_ROIs.md'
- CellType Proportion Exploration: 'tutorials/archive/4-CellType_Proportion_Exploration.md'
- Simple Spatial Analysis: 'tutorials/archive/5-Simple_Spatial_Analysis.md'
- Animate with scimap: 'tutorials/archive/6_animate_with_scimap.md'
- Contribute: 'contribute.md'
plugins:
- mkdocstrings:
handlers:
python:
options:
heading_level: 4
- search:
prebuild_index: true
- autorefs
markdown_extensions:
- admonition
- codehilite
- pymdownx.superfences
- pymdownx.inlinehilite
- footnotes
- meta
- tables
- markdown.extensions.tables
- pymdownx.highlight:
linenums: true
extra_css:
- stylesheets/extra.css
copyright: Copyright © 2024 | Nirmal Lab | www.nirmallab.com
extra:
generator: false
analytics:
provider: google
property: G-22X9HCL4YP
social:
- icon: fontawesome/brands/twitter
link: https://twitter.com/nirmallab
name: Twitter