MDSplot {ViSEAGO} | R Documentation |
Generate a Multi Dimensional Scale (MDS) plot from distance objects.
MDSplot(object, type = "GOterms", file = NULL) ## S4 method for signature 'ANY' MDSplot(object, type = "GOterms", file = NULL)
object |
a |
type |
could be "GOterms" to display GOterms MDSplot, or "GOclusters" to display GOclusters MDSplot. |
file |
static image output file name (default to NULL). |
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.
a MDS plot.
# 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,"GOterms") # 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)