Get Cnet node set by connected Sets

Get Cnet node set by connected Sets, using nodeType to delineate the two types of nodes in the graph.

Usage

get_cnet_nodeset(g, set_nodes = NULL, sep = ",", filter_set_only = TRUE, ...)

Arguments

g

igraph object specifically containing Cnet plot data, with node attribute "nodeType" that has values c("Gene", "Set").

set_nodes

character vector, default NULL, used to subset the returned data to nodes which are connected to these 'Set' nodes. of one or more set names, which are defined here as the names of the nodes with nodeType="Set" to which each node with nodeType="Gene" is connected. For example set_nodes=c("A", "B") will return all Gene nodes that are connected only to Set nodes "A" and "B". If set_nodes=NULL then this function returns a list with all set_nodes observed.

sep

character string used as a delimited when combining set_nodes into a name.

filter_set_only

logical default TRUE, whether to exclude Set nodes, with vertex attribute nodeType='Set', from being members of nodegroups. In principle, 'Gene' nodes are typically members of Cnet nodesets, and 'Set' nodes do not usually share the same 'Gene' nodes with other 'Set' nodes, and therefore are not included.

...

additional arguments are ignored.

Value

list named by nodeset, with character vectors of node names in each nodeset. When filter_set_only=TRUE by default, the nodes will not contain 'Set' nodes. The list is named by nodes connected by nodes in each node group, using sep as delimiter.

Details

This function operates on a Cnet igraph object, distinguished by node attribute 'nodeType' with values: 'Gene' for Gene nodes, and 'Set' for Set nodes. This function returns Gene nodes that are connected to the Sets given by argument set_nodes. It is useful to identify which genes are connected to Set "A" and "B" for example, in other words the Gene nodes in a specific subcluster of the Cnet igraph.

When set_nodes is NULL, this function returns a list containing character vectors, where each vector represents Gene nodes that are connected to each combination of Set nodes. This option is useful for obtaining all possible Gene subclusters.

This function is also called by adjust_cnet_nodeset() in order to manipulate all nodes in a subcluster as a group, for example calling nudge_igraph_node() on the whole set of nodes.

Note that when input data do not contain vertex attribute 'nodeType', data are still returned but cannot be filtered by 'Set' and 'Gene', and so will contain all possible node-connection groupings.

See also

Other jam igraph utilities: color_edges_by_nodegroups(), color_edges_by_nodes(), color_nodes_by_nodegroups(), jam_igraph(), launch_shinycat(), subgraph_jam()

Other jam cnet utilities: adjust_cnet_nodeset(), adjust_cnet_set_relayout_gene(), apply_nodeset_spacing(), bulk_cnet_adjustments(), get_cnet_nodeset_vector(), launch_shinycat(), make_cnet_test(), relayout_nodegroups()

Examples

cnet1 <- make_cnet_test()
get_cnet_nodeset(cnet1)
#> $SetA
#>  [1] "AB" "AO" "AV" "AW" "BE" "F"  "H"  "J"  "K"  "M"  "O"  "Q"  "R"  "W"  "X" 
#> [16] "Y" 
#> 
#> $`SetA,SetB`
#> [1] "BH" "BT" "BU"
#> 
#> $`SetA,SetB,SetC,SetD`
#> [1] "CL" "CM" "CN" "CO" "CP"
#> 
#> $`SetA,SetB,SetD`
#> [1] "BZ" "CD" "CI"
#> 
#> $`SetA,SetC`
#> [1] "BR" "BS" "BY"
#> 
#> $`SetA,SetC,SetD`
#> [1] "CB" "CC" "CE" "CF" "CG" "CJ" "CK"
#> 
#> $`SetA,SetD`
#> [1] "BK" "BL" "BN" "BQ"
#> 
#> $SetB
#>  [1] "AK" "AL" "AP" "AR" "AS" "AT" "BC" "C"  "D"  "E"  "I"  "P"  "V"  "Z" 
#> 
#> $`SetB,SetC`
#> [1] "BG" "BM" "BO" "BV"
#> 
#> $`SetB,SetC,SetD`
#> [1] "CA" "CH"
#> 
#> $`SetB,SetD`
#> [1] "BF" "BJ" "BP" "BW" "BX"
#> 
#> $SetC
#>  [1] "A"  "AC" "AD" "AE" "AH" "AI" "AN" "AU" "AX" "AY" "AZ" "BA" "BB" "G"  "L" 
#> [16] "N"  "T"  "U" 
#> 
#> $`SetC,SetD`
#> [1] "BI"
#> 
#> $SetD
#> [1] "AA" "AF" "AG" "AJ" "AM" "AQ" "B"  "BD" "S" 
#> 

get_cnet_nodeset(cnet1, c("SetB,SetD"))
#> $`SetB,SetD`
#> [1] "BF" "BJ" "BP" "BW" "BX"
#>