# 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

 ```1 2``` ```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

 ``` 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``` ```## 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 May 2, 2018, 3:33 a.m.