sc_ComparissonOfGraphs: Comparisson of graphs

In sincell: R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

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))

sincell documentation built on Nov. 8, 2020, 5:58 p.m.