dDAGannotate 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 "graphNET" 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 gene
annotated to a term should also be annotated by its all ancestor terms.
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an object of class "igraph" or "graphNEL"
the vertices/nodes for which annotation data are provided
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". 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 genes either as original annotations or inherited
annotations; "IC", which stands for information content defined as
negative 10-based log-transformed frequency of genes annotated to that
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 HPPA as igraph object ig.HPPA <-dRDataLoader(RData='ig.HPPA') g <- ig.HPPA # 2) load human genes annotated by HPPA org.Hs.egHPPA <- dRDataLoader(RData='org.Hs.egHPPA') GS <- org.Hs.egHPPA # as 'GS' object # 3) prepare for annotation data # randomly select vertices with annotation data annotations <- GS$gs[sample(1:length(GS$gs),5)] # 4) obtain the induced subgraph # 4a) based on all possible paths (i.e. the complete subgraph induced) dDAGannotate(g, annotations, path.mode="all_paths", verbose=TRUE) # 4b) based on shortest paths (i.e. the most concise subgraph induced) dag <- dDAGannotate(g, annotations, path.mode="shortest_paths", verbose=TRUE) # 5) color-code nodes/terms according to the number of annotations data <- sapply(V(dag)$annotations, length) names(data) <- V(dag)$name visDAG(g=dag, data=data, node.info="both") ## End(Not run)
Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: supraHex Loading required package: hexbin 'ig.HPPA' (from package 'dnet' version 1.1.4) has been loaded into the working environment (at 2020-10-21 03:33:19) 'org.Hs.egHPPA' (from package 'dnet' version 1.1.4) has been loaded into the working environment (at 2020-10-21 03:33:20) At level 8, there are 1 nodes, and 1 incoming neighbors. At level 7, there are 2 nodes, and 2 incoming neighbors. At level 6, there are 3 nodes, and 3 incoming neighbors. At level 5, there are 3 nodes, and 3 incoming neighbors. At level 4, there are 5 nodes, and 5 incoming neighbors. At level 3, there are 5 nodes, and 5 incoming neighbors. At level 2, there are 5 nodes, and 1 incoming neighbors. At level 1, there are 1 nodes, and 0 incoming neighbors. IGRAPH cd90264 DN-- 25 24 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), annotations (v/x), IC (v/n), relation (e/c) + edges from cd90264 (vertex names):  HP:0000118->HP:0000152 HP:0000118->HP:0000478 HP:0000118->HP:0000598  HP:0000118->HP:0000924 HP:0000118->HP:0002715 HP:0000152->HP:0000234  HP:0000478->HP:0012372 HP:0000598->HP:0000356 HP:0000924->HP:0011842  HP:0002715->HP:0010978 HP:0012372->HP:0012374 HP:0000234->HP:0000271  HP:0000356->HP:0000377 HP:0010978->HP:0002960 HP:0011842->HP:0003330  HP:0000271->HP:0000366 HP:0002960->HP:0030057 HP:0012374->HP:0004328  HP:0030057->HP:0003493 HP:0000366->HP:0010938 HP:0004328->HP:0000481 + ... omitted several edges At level 8, there are 1 nodes, and 1 incoming neighbors. At level 7, there are 2 nodes, and 2 incoming neighbors. At level 6, there are 3 nodes, and 3 incoming neighbors. At level 5, there are 3 nodes, and 3 incoming neighbors. At level 4, there are 5 nodes, and 5 incoming neighbors. At level 3, there are 5 nodes, and 5 incoming neighbors. At level 2, there are 5 nodes, and 1 incoming neighbors. At level 1, there are 1 nodes, and 0 incoming neighbors.
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