Description Usage Arguments Value Examples

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.

1 2 | ```
sc_ComparissonOfGraphs(cellstateHierarchy1,cellstateHierarchy2, ...,
graph.names=NULL)
``` |

`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. |

A distance matrix comparing the graphs.

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 31, 2017, 11:18 a.m.

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