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Print OmniPath interactions

Source: R/print_interactions.R
print_interactions.Rd

Prints the interactions or enzyme-substrate relationships in a nice format.

Usage

print_interactions(interactions, refs = FALSE)

Arguments

interactions

Data frame with the interactions generated by any of the functions in omnipath-interactions.

refs

Logical: include PubMed IDs where available.

Value

Returns `NULL`.

Examples

enzsub <- enzyme_substrate()
print_interactions(head(enzsub))
#> Warning: Unknown or uninitialised column: `is_stimulation`.
#> # A tibble: 6 × 5
#>   enzyme       interaction substrate           modification    n_resources
#>   <chr>        <chr>       <chr>               <chr>                 <int>
#> 1 SRC (P12931) ====>       TERT_Y707 (O14746)  phosphorylation           8
#> 2 FYN (P06241) ====>       FYB1_Y595 (O15117)  phosphorylation           7
#> 3 LCK (P06239) ====>       SOCS3_Y221 (O14543) phosphorylation           6
#> 4 FYN (P06241) ====>       FYB1_Y651 (O15117)  phosphorylation           6
#> 5 FYN (P06241) ====>       FYB1_Y697 (O15117)  phosphorylation           3
#> 6 LCK (P06239) ====>       SOCS3_Y204 (O14543) phosphorylation           6
print_interactions(tail(enzsub), refs = TRUE)
#> Warning: Unknown or uninitialised column: `is_stimulation`.
#> # A tibble: 6 × 7
#>   enzyme  interaction substrate modification n_resources n_references references
#>   <chr>   <chr>       <chr>     <chr>              <int>        <dbl> <chr>     
#> 1 TYRO3 … ====>       PLCG1_Y7… phosphoryla…           1            8 KEA:12601…
#> 2 TYK2 (… ====>       STAT5B_Y… phosphoryla…           1            3 KEA:10830…
#> 3 TYK2 (… ====>       IL13RA1_… phosphoryla…           1            1 KEA:10409…
#> 4 WNK1 (… ====>       OSR1_T18… phosphoryla…           1            1 KEA:18270…
#> 5 WNK1 (… ====>       WNK4_S33… phosphoryla…           1            1 KEA:15883…
#> 6 MAP3K2… ====>       CDS1_T68… phosphoryla…           1            1 KEA:10973…
print_interactions(
    dplyr::filter(
        enzsub,
        enzyme_genesymbol == 'MAP2K1',
        substrate_genesymbol == 'MAPK3'
    )
)
#> Warning: Unknown or uninitialised column: `is_stimulation`.
#> # A tibble: 6 × 5
#>   enzyme          interaction substrate           modification    n_resources
#>   <chr>           <chr>       <chr>               <chr>                 <int>
#> 1 MAP2K1 (Q02750) ====>       MAPK3_Y204 (P27361) phosphorylation           8
#> 2 MAP2K1 (Q02750) ====>       MAPK3_T202 (P27361) phosphorylation           8
#> 3 MAP2K1 (Q02750) ====>       MAPK3_T207 (P27361) phosphorylation           2
#> 4 MAP2K1 (Q02750) ====>       MAPK3_Y210 (P27361) phosphorylation           2
#> 5 MAP2K1 (Q02750) ====>       MAPK3_T80 (P27361)  phosphorylation           1
#> 6 MAP2K1 (Q02750) ====>       MAPK3_Y222 (P27361) phosphorylation           1

signor <- omnipath(resources = "SIGNOR")
print_interactions(head(signor))
#> # A tibble: 6 × 5
#>   source          interaction target          n_resources n_references
#>   <chr>           <chr>       <chr>                 <int>        <int>
#> 1 PRKG1 (Q13976)  ==( - )==>  TRPC3 (Q13507)            8            2
#> 2 PTPN1 (P18031)  ==( - )==>  TRPV6 (Q9H1D0)            6            2
#> 3 PRKACA (P17612) ==( - )==>  MCOLN1 (Q9GZU1)           6            1
#> 4 PRKG1 (Q13976)  ==( + )==>  TRPC7 (Q9HCX4)            3            1
#> 5 OS9 (Q13438)    ==(+/-)==>  TRPV4 (Q9HBA0)            3            1
#> 6 RACK1 (P63244)  ==( - )==>  TRPM6 (Q9BX84)            2            1
#            source interaction            target n_resources
# 6 MAPK14 (Q16539)  ==( + )==> MAPKAPK2 (P49137)          23
# 4  TRPM7 (Q96QT4)  ==( + )==>    ANXA1 (P04083)          10
# 1  PRKG1 (Q13976)  ==( - )==>    TRPC3 (Q13507)           8
# 2  PTPN1 (P18031)  ==( - )==>    TRPV6 (Q9H1D0)           6
# 5 PRKACA (P17612)  ==( - )==>   MCOLN1 (Q9GZU1)           6
# 3  RACK1 (P63244)  ==( - )==>    TRPM6 (Q9BX84)           2