bioDistWPlot {STATegRa} | R Documentation

## bioDistWPlot

### Description

Function that plots the "distance relation" between features computed through different surrogate features.

### Usage

    bioDistWPlot(referenceFeatures, listDistW, method.cor)

### Arguments

`referenceFeatures` | The set of features to be used.
`listDistW` | A list of bioDistWclass objects.
`method.cor` | Method to compute distances between the elements in the listDistW. The default is spearman correlation.

### Value

Makes a plot with the projected distance between the listDistW objects.

### Author(s)

David Gomez-Cabrero

### Examples

    data(STATegRa_S1)
    data(STATegRa_S2)
    require(Biobase)

    # Truncate data for brevity
    Block1 <- Block1[1:100,]
    Block2 <- Block2[1:100,]

    ## Create ExpressionSets
    mRNA.ds <- createOmicsExpressionSet(Data=Block1,pData=ed,pDataDescr=c("classname"))
    miRNA.ds <- createOmicsExpressionSet(Data=Block2,pData=ed,pDataDescr=c("classname"))

    ## Create the bioMap
    map.gene.miRNA<-bioMap(name = "Symbol-miRNA",
                           metadata =  list(type_v1="Gene",type_v2="miRNA",
                                            source_database="targetscan.Hs.eg.db",
                                            data_extraction="July2014"),
                           map=mapdata)

    # Create Gene-gene distance computed through miRNA data
    bioDistmiRNA<-bioDist(referenceFeatures = rownames(Block1),
                          reference = "Var1",
                          mapping = map.gene.miRNA,
                          surrogateData = miRNA.ds,  ### miRNA data
                          referenceData = mRNA.ds,  ### mRNA data
                          maxitems=2,
                          selectionRule="sd",
                          expfac=NULL,
                          aggregation = "sum",
                          distance = "spearman",
                          noMappingDist = 0,
                          filtering = NULL,
                          name = "mRNAbymiRNA")

    # Create Gene-gene distance through mRNA data
    bioDistmRNA<-new("bioDistclass",
                     name = "mRNAbymRNA",
                     distance = cor(t(exprs(mRNA.ds)),method="spearman"),
                     map.name = "id",
                     map.metadata = list(),
                     params = list())

    ###### Generation of the list of Surrogated distances.

    bioDistList<-list(bioDistmRNA,bioDistmiRNA)
    sample.weights<-matrix(0,4,2)
    sample.weights[,1]<-c(0,0.33,0.67,1)
    sample.weights[,2]<-c(1,0.67,0.33,0)

    ###### Generation of the list of bioDistWclass objects.

    bioDistWList<-bioDistW(referenceFeatures = rownames(Block1),
                           bioDistList = bioDistList,
                           weights=sample.weights)

    ###### Plot of distances.
    bioDistWPlot(referenceFeatures = rownames(Block1) ,
                 listDistW = bioDistWList,
                 method.cor="spearman")

    ###### Computing the matrix of features/distances associated.

    fm<-bioDistFeature(Feature = rownames(Block1)[1] ,
                       listDistW = bioDistWList,
                       threshold.cor=0.7)
    bioDistFeaturePlot(data=fm)

[Package STATegRa version 1.20.0 Index]