Multi Dimensional Scale (MDS) plot

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

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)