bioDistWPlot: bioDistWPlot

In lunacab/STATegRa: Classes and methods for multi-omics data integration

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)

lunacab/STATegRa documentation built on May 5, 2019, 2:42 a.m.