sc_ComparissonOfGraphs {sincell} | R Documentation

## Comparisson of graphs

### Description

Function to assess a distance matrix comparing the graphs from Sincell objects that were generated with function sc_GraphBuilderObj(). The distance between two graphs is assessed as 1 minus their similarity, which is calculated as the spearman rank correlation between the two graphs of the shortest distance for all pairs of cells. Cell-state hierarchies are igraph graph objects (see "igraph" R package documentation) representing a totally connected graph.

### Usage

    sc_ComparissonOfGraphs(cellstateHierarchy1,cellstateHierarchy2, ...,
      graph.names=NULL)

### Arguments

`cellstateHierarchy1` | A first cell-state hierarchy as created by function sc_GraphBuilderObj() on a SincellObject.
`cellstateHierarchy2` | A second cell-state hierarchy as created by function sc_GraphBuilderObj() on a SincellObject.
`...` | Further cell-state hierarchies
`graph.names` | A vector of characters indicating the names of the cell-state hierarchies provided as arguments.

### Value

A distance matrix comparing the graphs.

### Examples

    ## Generate some random data
    Data <- matrix(abs(rnorm(3000, sd=2)),ncol=10,nrow=30)

    ## Initializing SincellObject
    mySincellObject <- sc_InitializingSincellObject(Data)

    ## Assessmet of cell-to-cell distance matrix after dimensionality reduction
    ## with Principal Component Analysis (PCA), with Independent Component
    ## Analysis (ICA), or with non-metric Multidimensional Scaling (nonmetric-MDS)
    mySincellObject_PCA <- sc_DimensionalityReductionObj(mySincellObject,
      method="PCA",dim=2)
    mySincellObject_ICA <- sc_DimensionalityReductionObj(mySincellObject,
      method="ICA",dim=2)
    mySincellObject_classicalMDS <- sc_DimensionalityReductionObj(mySincellObject,
      method="classical-MDS",dim=2)
    mySincellObject_nonmetricMDS <- sc_DimensionalityReductionObj(mySincellObject,
      method="nonmetric-MDS",dim=2)

    ## Assessment of cell-state hierarchy
    mySincellObject_PCA<- sc_GraphBuilderObj(mySincellObject_PCA,
      graph.algorithm="SST")
    mySincellObject_ICA<- sc_GraphBuilderObj(mySincellObject_ICA,
      graph.algorithm="SST")
    mySincellObject_classicalMDS<- sc_GraphBuilderObj(mySincellObject_classicalMDS,
      graph.algorithm="SST")
    mySincellObject_nonmetricMDS<- sc_GraphBuilderObj(mySincellObject_nonmetricMDS,
      graph.algorithm="SST")

    ## Comparisson of hierarchies obtained from different methods
    myComparissonOfGraphs<-sc_ComparissonOfGraphs(
      mySincellObject_PCA[["cellstateHierarchy"]],
      mySincellObject_ICA[["cellstateHierarchy"]],
      mySincellObject_classicalMDS[["cellstateHierarchy"]],
      mySincellObject_nonmetricMDS[["cellstateHierarchy"]],
      graph.names=c("PCA","ICA","classicalMDS","nonmetricMDS")
      )
    plot(hclust(myComparissonOfGraphs))

[Package sincell version 1.12.0 Index]