dcDAGannotate is supposed to produce a subgraph induced by the
input annotation data, given a direct acyclic graph (DAG; an ontology).
The input is a graph of "igraph" or "Onto" object, a list of the
vertices containing annotation data, and the mode defining the paths to
the root of DAG. The induced subgraph contains vertices (with
annotation data) and their ancestors along with the defined paths to
the root of DAG. The annotations at these vertices (including their
ancestors) are also updated according to the true-path rule: a domain
annotated to a term should also be annotated by its all ancestor terms.
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an object of class "igraph" or
an object of class
the mode of paths induced by vertices/nodes with input annotation data. It can be "all_paths" for all possible paths to the root, "shortest_paths" for only one path to the root (for each node in query), "all_shortest_paths" for all shortest paths to the root (i.e. for each node, find all shortest paths with the equal lengths)
logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
subg: an induced subgraph, an object of class "igraph" or
"Onto" (the same as input). In addition to the original attributes to
nodes and edges, the return subgraph is also appended by new node
attributes: "annotations", which contains a list of domains either as
original annotations or inherited annotations; "IC", which stands for
information content defined as negative 10-based log-transformed
frequency of domains annotated to that term.
For the mode "shortest_paths", the induced subgraph is the most concise, and thus informative for visualisation when there are many nodes in query, while the mode "all_paths" results in the complete subgraph.
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## Not run: # 1) load onto.GOMF (as 'Onto' object) g <- dcRDataLoader('onto.GOMF') # 2) load SCOP superfamilies annotated by GOMF (as 'Anno' object) Anno <- dcRDataLoader('SCOP.sf2GOMF') # 3) prepare for annotation data # randomly select 5 terms vertices (and their annotation data) annotations <- Anno[,sample(1:dim(Anno), 5)] # 4) obtain the induced subgraph according to the input annotation data # 4a) based on all possible paths (i.e. the complete subgraph induced) dcDAGannotate(g, annotations, path.mode="all_paths", verbose=TRUE) # 4b) based on shortest paths (i.e. the most concise subgraph induced) dag <- dcDAGannotate(g, annotations, path.mode="shortest_paths", verbose=TRUE) # 5) color-code nodes/terms according to the number of annotations if(class(dag)=='Onto') dag <- dcConverter(dag, from='Onto', to='igraph') data <- sapply(V(dag)$annotations, length) names(data) <- V(dag)$name dnet::visDAG(g=dag, data=data, node.info="both") ## End(Not run)
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