Produce a tidygraph network for a given cluster

Usage

produceNetworkForCluster(ingres.object, cluster.id)

Arguments

ingres.object: The ingres object containing the relevant data.
cluster.id: The id of the cluster for which the network is to be produced.

Value

A tidygraph object containing the network for the given cluster.

Examples

# Create an ingres object with viper slot
ing <- createIngresObjectFromSeurat(
  small_blca_wang, "RNA", "data", network_genes, network
)
ing@viper <- viper_results
#> Error in eval(expr, envir, enclos): object 'viper_results' not found

ing <- computePbnByCluster(ing)
#> Error in select(., c(1, 2)): Can't subset columns past the end.
#> ℹ Locations 1 and 2 don't exist.
#> ℹ There are only 0 columns.

network <- produceNetworkForCluster(ing, "1")
#> Error in filter(., .data$cluster == cluster.id): Problem while computing `..1 = .data$cluster == cluster.id`.
#> Caused by error in `.data$cluster`:
#> ! Column `cluster` not found in `.data`.
print(network)
#> # A tbl_graph: 30 nodes and 110 edges
#> #
#> # A directed multigraph with 1 component
#> #
#> # Node Data: 30 × 3 (active)
#>   kind  rule                              id              
#>   <chr> <chr>                             <chr>           
#> 1 input ""                                DNAdamage       
#> 2 input ""                                GrowthInhibitors
#> 3 fate  "CyclinE1 or CyclinA"             Proliferation   
#> 4 fate  "E2F1_2 or TP53"                  Apoptosis       
#> 5 fate  "p21CIP or RB1 or RBL2"           Growth_Arrest   
#> 6 gene  "SPRY and not FGFR3 and not GRB2" EGFR            
#> # … with 24 more rows
#> #
#> # Edge Data: 110 × 3
#>    from    to sign    
#>   <int> <int> <chr>   
#> 1     8    30 positive
#> 2    14     3 positive
#> 3    15     3 positive
#> # … with 107 more rows