_pkgdown.yml

template:
  params:
    bootswatch: flatly

home:
 links:
 - text: Visit us
   href: https://themilolab.com/

navbar:
   structure:
      left: [home, reference, about, installation, terminology, articles]
   components:
      about:
       text: About
       href: articles/about.html
      installation:
       text: Installation
       href: articles/installation.html
      terminology:
       text: Terminology
       href: articles/terminology.html
      articles:
       text: Articles
       menu: 
       - text: Getting started
       - text: 1. Experiment design 
         href: articles/design-experiment.html
       - text: 2. Data loading 
         href: articles/load-data.html
       - text: 3. Data processing
         href: articles/process-data.html
       - text: Quality checks
       - text: Outlier detection 
         href: articles/outlier-detection.html
       - text: Around the cypro object
       - text: Default setting 
         href: articles/default-setting.html
       - text: Create data subsets
         href: articles/subsetting.html
       - text: Extract data and information
         href: articles/extract-data.html
       - text: Add content 
         href: articles/adding.html
       - text: Rename content
         href: articles/renaming.html
       - text: Variable sets 
         href: articles/variable-sets.html
       - text: Cell Profiling
       - text: Dimensionality reduction
         href: articles/dim-red.html
       - text: Correlation
         href: articles/correlation.html
       - text: Clustering
         href: articles/clustering.html
       - text: Analysis Modules
       - text: Migration
         href: articles/module-migration.html
       - text: Visualization
       - text: Statistical tests and plots
         href: articles/plotting-stats.html

reference:

 - title: Object Initiation
   desc: Three functions are needed to set up a fully functional cypro object.
 - contents:
   - designExperiment
   - starts_with("loadDataFil")
   - processData
   
 - title: Object Summary and Information 
   desc: Keep track of progress and set up by printing summaries in the console. 
 - contents: 
   - starts_with("print")

 - title: Object Loading and Saving
   desc: Some handy functions that make saving and loading corresponding objects more convenient.
 - contents:
   - starts_with("save")


 - title: Object Subsetting
   desc: Create cypro object from data subsets for more in depth analysis.
 - contents:
   - starts_with("subsetBy")
   

 - title: Object Manipulation
   desc: cypro invites you to extract your analysis and to add the results of your
         analysis. Constant change of the object's content is therefore inevitable. The following
         functions serve as handy, helping hands to add cypro extern content to the object
         without disturbing it's integrity regarding cypro intern processes.

 - subtitle: Set Content
   desc: The set-functions let you set the content of specific slots.
 - contents:
   - starts_with("set")
   - -starts_with("set_")
   - -starts_with("setUp")

 - subtitle: Add Content
   desc: The add-functions let you add content to the cypro object.
 - contents:
   - starts_with("add")
   - -starts_with("add_")

 - subtitle: Discard Content
   desc: The discard-functions let you delete unwanted information savely.
 - contents:
   - starts_with("discard")

 - subtitle: Adjust Content
   desc: The adjust-functions let you adjust content of the cypro object without overwriting it in it's essence.
 - contents:
   - starts_with("adjust")

 - subtitle: Rename Content
   desc: The rename-functions let you adjust the names of data variables and of groups.
 - contents:
   - starts_with("rename")

 - title: Extract Data
   desc: cypro invites you to extract your analysis. get-functions let you access every imaginable aspect of information conveniently.

 - subtitle: Data frames
   desc: A lot of data comes in form of tidy data.frames. 
 - contents:
   - ends_with("Df")
   - -starts_with("rename")
   - -starts_with("set")
   
 - subtitle: Data variable names and group names
   desc: Functions that return object dependent input options for different arguments. 
 - contents:
   - ends_with("VariableNames")
   - getGroupNames
   
 - subtitle: Names and content of variable sets 
   desc: Keep track of your data variables by gathering them to variable sets. 
 - contents:
   - contains("VariableSet")
   - -starts_with("add")
   
 - subtitle: Analysis results 
   desc: Extract analysis results for cypro extern analysis. 
 - contents: 
   - getHclustObject
   - getKmeansObject
   - getPamObject
   - getCorrObject
   - getPcaObject
   - getTsneObject
   - getUmapObject
   
 - subtitle: Outlier detection
 - contents: 
   - starts_with("getOutlier")
   
 - subtitle: Miscellaneous
 - contents: 
   - starts_with("n")

 - title: Quality Check 
   desc: Clean your data before conducting analysis with common quality checks. 
 - subtitle: Outlier detection
 - contents: 
   - detectOutliers
   - removeOutliers
 - subtitle: Batch effect detection
 - contents:
   - detectBatchEffects
   - plotBatchHeatmap

 - title: Analysis and Profiling 
   desc: Leverage convenient implementations of several machine learning algorithms 
         to cluster and profile your cells. 
 - subtitle: Dimensional reduction
 - contents: 
   - runPca
   - runTsne
   - runUmap
 - subtitle: Clustering 
 - contents: 
   - initiateKmeansClustering
   - initiateHierarchicalClustering
   - initiatePamClustering
   - computeDistanceMatrices
   - agglomerateHierarchicalCluster
   - computeKmeansCluster
   - computePamCluster
 - subtitle: Correlation
 - contents: 
   - initiateCorrelation
   - correlateAll
   - correlateAcross
   
 - title: Visualization and Animation
 - subtitle: Statistics and common plots 
 - contents: 
   - plotBoxplot 
   - plotViolinplot
   - plotHistogram
   - plotDensityplot
   - plotRidgeplot
   - plotStatisticsInteractive
   - plotScatterplot
   
 - subtitle: Dimensional reduction
 - contents: 
   - plotPca
   - plotTsne 
   - plotUmap 

 - subtitle: Clustering 
 - contents:
   - plotScreeplot
   - plotAvgSilhouetteWidths
   - plotSilhouetteWidths
   - plotPamMedoids
   
 - subtitle: Timelapse dependent
 - contents:
   - starts_with("plotTime")
  
 - title: Modules
   desc: Depending on the experiment set up and the data input different modules (collections of functions)
         are at your your disposal.
         
 - subtitle: Migration
   desc: In case of timelapse experiments that come with x- and y-coordinates you can explore cellular migration 
         behaviour.
 - contents: 
   - plotSingleTracks
   - plotAllTracks 
   - animateAllTracks
   
   
 - title: Valid argument input 
   desc: Functions that don't take any argument specifications but simply return valid input options 
         for several arguments. 
 - contents: 
   - starts_with("valid")
   - -starts_with("valid_")
   - -starts_with("validate_")