MDSplot-methods: Multi Dimensional Scale (MDS) plot

In abrionne/ViSEAGO: ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity

Description

Generate a Multi Dimensional Scale (MDS) plot from distance objects.

Usage

MDSplot(object, type = "GOterms", file = NULL)

## S4 method for signature 'ANY'
MDSplot(object, type = "GOterms", file = NULL)

Arguments

object	a GO_SS-class or GO_clusters-class objects from distances computed with compute_SS_distances.
type	could be "GOterms" to display GOterms MDSplot, or "GOclusters" to display GOclusters MDSplot.
file	static image output file name (default to NULL).

Details

This method build and display the javascript MDSplot (if file=NULL) from GO_SS-class or GO_clusters-class objects.
A static png image could be printed by setting file argument.

Value

a MDS plot.

Examples

###################
# load data example
utils::data(
 myGOs,
 package="ViSEAGO"
)
## Not run: 
###################
# compute GO terms Semantic Similarity distances
myGOs<-ViSEAGO::compute_SS_distances(
    myGOs,
    distance="Wang"
)

###################
# build MDS plot for a GO_SS-class distance object
ViSEAGO::MDSplot(myGOs)

##################
# GOtermsHeatmap with default parameters
Wang_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
    myGOs,
    showIC=TRUE,
    showGOlabels=TRUE,
    GO.tree=list(
        tree=list(
            distance="Wang",
            aggreg.method="ward.D2",
            rotate=NULL
        ),
        cut=list(
            dynamic=list(
                pamStage=TRUE,
                pamRespectsDendro=TRUE,
                deepSplit=2,
                minClusterSize =2
            )
        )
    ),
    samples.tree=NULL
)

###################
# build MDS plot for a GO_clusters-class distance object, highlighting GO terms clusters.
ViSEAGO::MDSplot(
    Wang_clusters_wardD2,
    "GOterms"
)

###################
# compute clusters of GO terms Semantic Similarity distances
Wang_clusters_wardD2<-ViSEAGO::compute_SS_distances(
    Wang_clusters_wardD2,
    distance="BMA"
)

###################
# GOclusters heatmap
Wang_clusters_wardD2<-ViSEAGO::GOclusters_heatmap(
    Wang_clusters_wardD2,
    tree=list(
        distance="BMA",
        aggreg.method="ward.D2",
        rotate=NULL
    )
)

###################
# build MDS plot for a GO_clusters-class distance object, highlighting GO groups clusters.
ViSEAGO::MDSplot(
    Wang_clusters_wardD2,
    "GOclusters"
)

## End(Not run)

abrionne/ViSEAGO documentation built on June 13, 2019, 2:27 p.m.