Prints the interactions or enzyme-substrate relationships in a nice format.
Arguments
- interDF
data.frame with the interactions generated by any of the following functions:
- writeRefs
[FALSE] writes also the PubMed IDs if available
Examples
enzsub <- import_omnipath_enzsub()
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), writeRefs = TRUE)
#> Warning: Unknown or uninitialised column: `is_stimulation`.
#> # A tibble: 6 × 7
#> enzyme interaction substrate modif…¹ n_res…² n_ref…³ refer…⁴
#> <chr> <chr> <chr> <chr> <int> <dbl> <chr>
#> 1 TYRO3 (Q06418) ====> PLCG1_Y771 (P191… phosph… 1 8 KEA:12…
#> 2 TYK2 (P29597) ====> STAT5B_Y699 (P51… phosph… 1 3 KEA:10…
#> 3 TYK2 (P29597) ====> IL13RA1_Y402 (P7… phosph… 1 1 KEA:10…
#> 4 WNK1 (Q9H4A3) ====> OSR1_T185 (Q8TAX… phosph… 1 1 KEA:18…
#> 5 WNK1 (Q9H4A3) ====> WNK4_S335 (Q96J9… phosph… 1 1 KEA:15…
#> 6 MAP3K20 (Q9NYL2) ====> CDS1_T68 (Q92903) phosph… 1 1 KEA:10…
#> # … with abbreviated variable names ¹modification, ²n_resources, ³n_references,
#> # ⁴references
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 <- import_omnipath_interactions(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