compare_clusters {ViSEAGO} | R Documentation |
Build an interactive heatmap of the common GO terms frequency between several partitions.
compare_clusters(clusters) ## S4 method for signature 'list' compare_clusters(clusters)
clusters |
a |
Build an interactive heatmap of common GO terms frequency between partitions from several
GO_clusters-class
objects.
an interactive javascript heatmap.
Carson Sievert, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. https://CRAN.R-project.org/package=plotly
Other GO_clusters:
GO_clusters-class
,
GOclusters_heatmap()
,
clusters_cor()
,
show_heatmap()
,
show_table()
# load example object data( myGOs, package="ViSEAGO" ) ## Not run: # compute Semantic Similarity (SS) myGOs<-ViSEAGO::compute_SS_distances( myGOs, distance=c("Resnik","Lin","Rel","Jiang","Wang") ) # Resnik distance GO terms heatmap Resnik_clusters_wardD2<-ViSEAGO::GOterms_heatmap( myGOs, showIC=TRUE, showGOlabels=TRUE, GO.tree=list( tree=list( distance="Resnik", aggreg.method="ward.D2" ), cut=list( dynamic=list( deepSplit=2, minClusterSize =2 ) ) ), samples.tree=NULL ) # Lin distance GO terms heatmap Lin_clusters_wardD2<-ViSEAGO::GOterms_heatmap( myGOs, showIC=TRUE, showGOlabels=TRUE, GO.tree=list( tree=list( distance="Lin", aggreg.method="ward.D2" ), cut=list( dynamic=list( deepSplit=2, minClusterSize =2 ) ) ), samples.tree=NULL ) # Resnik distance GO terms heatmap Rel_clusters_wardD2<-ViSEAGO::GOterms_heatmap( myGOs, showIC=TRUE, showGOlabels=TRUE, GO.tree=list( tree=list( distance="Rel", aggreg.method="ward.D2" ), cut=list( dynamic=list( deepSplit=2, minClusterSize =2 ) ) ), samples.tree=NULL ) # Resnik distance GO terms heatmap Jiang_clusters_wardD2<-ViSEAGO::GOterms_heatmap( myGOs, showIC=TRUE, showGOlabels=TRUE, GO.tree=list( tree=list( distance="Jiang", aggreg.method="ward.D2" ), cut=list( dynamic=list( deepSplit=2, minClusterSize =2 ) ) ), samples.tree=NULL ) # Resnik distance GO terms heatmap Wang_clusters_wardD2<-ViSEAGO::GOterms_heatmap( myGOs, showIC=TRUE, showGOlabels=TRUE, GO.tree=list( tree=list( distance="Wang", aggreg.method="ward.D2" ), cut=list( dynamic=list( deepSplit=2, minClusterSize =2 ) ) ), samples.tree=NULL ) ## End(Not run) # clusters to compare clusters<-list( Resnik="Resnik_clusters_wardD2", Lin="Lin_clusters_wardD2", Rel="Rel_clusters_wardD2", Jiang="Jiang_clusters_wardD2", Wang="Wang_clusters_wardD2" ) ## Not run: # clusters content comparisons clusters_comp<-ViSEAGO::compare_clusters(clusters) ## End(Not run)