MDSplot {ViSEAGO} | R Documentation

## 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

`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)

[Package ViSEAGO version 1.0.0 Index]