print_interactions: Print OmniPath interactions

In saezlab/OmnipathR: OmniPath web service client and more

Print OmniPath interactions

Description

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

Usage

print_interactions(interDF, writeRefs = FALSE)

Arguments

interDF

data.frame with the interactions generated by any of the following functions: import_omnipath_enzsub import_omnipath_interactions import_pathwayextra_interactions import_kinaseextra_interactions import_ligrecextra_interactions import_post_translational_interactions import_dorothea_interactions import_tf_target_interactions import_transcriptional_interactions import_mirnatarget_interactions import_all_interactions

writeRefs

[FALSE] writes also the PubMed IDs if available

Value

Returns 'NULL'.

Examples

enzsub <- import_omnipath_enzsub()
print_interactions(head(enzsub))
print_interactions(tail(enzsub), writeRefs = TRUE)
print_interactions(
    dplyr::filter(
        enzsub,
        enzyme_genesymbol == 'MAP2K1',
        substrate_genesymbol == 'MAPK3'
    )
)

signor <- import_omnipath_interactions(resources = 'SIGNOR')
print_interactions(head(signor))
#            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

saezlab/OmnipathR documentation built on May 3, 2024, 5:32 a.m.