show_heatmap {ViSEAGO} | R Documentation |
Display a heatmap in interactive or static mode.
show_heatmap(object, type, file = NULL) ## S4 method for signature 'GO_clusters,character' show_heatmap(object, type, file = NULL)
object |
a |
type |
could be "GOterms" to display GOterms clustering heatmap, or "GOclusters" to display GOclusters heatmap. |
file |
static image output file name (default to NULL). |
This method displays an interactive heatmap (if file
=NULL) from GO_clusters-class
object for "GOterms" or "GOclusters" type.
A static png image could be printed by setting file
argument.
display or print heatmap.
Other enrich_GO_terms:
Upset()
,
enrich_GO_terms-class
,
overLapper()
,
show_table()
Other GO_clusters:
GO_clusters-class
,
GOclusters_heatmap()
,
clusters_cor()
,
compare_clusters()
,
show_table()
Other visualization:
GOclusters_heatmap()
,
GOcount()
,
GOterms_heatmap()
,
Upset()
,
available_organisms()
,
overLapper()
,
show_table()
# load data example 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 ) # Display GO terms heatmap ViSEAGO::show_heatmap( Wang_clusters_wardD2, "GOterms" ) # Print GO terms heatmap ViSEAGO::show_heatmap( Wang_clusters_wardD2, "GOterms", "GOterms_heatmap.png" ) # 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 ) ) # Display GO clusters heatmap ViSEAGO::show_heatmap( Wang_clusters_wardD2, "GOclusters" ) # Print GO clusters heatmap ViSEAGO::show_heatmap( Wang_clusters_wardD2, "GOclusters", "GOclusters_heatmap.png" ) ## End(Not run)