Dear all, I'm trying to figure out how to use the col.interactions.types parameters from the GenomicInteractions package to specifically color annotated interactions in the gviz plots. Here' s a little snippet showing how I annotate the interactions.

annotateInteractions(interactions,list(promoter=proms,enhancer=SE))
interaction_track <- InteractionTrack(interactions,name='HiC',chromosome = chr)
displayPars(interaction_track)  <- list(col.interactions="lightblue",
                                        col.interactions.types=c('promoter-distal'='red'))

I tryied to use

displayPars(interaction_track)  <- list(col.interactions="lightblue",
                                        col.interactions.types=c(pd='red'))

or

displayPars(interaction_track)  <- list(col.interactions="lightblue",
                                        col.interactions.types=c(is.pd='red'))

with not success. I'm not sure what names in the named vector are recognized. Any help would be appreciated.

thanks

Hi Marco,

There is a typo in the name of the display parameter you're setting - it should be col.interaction.types. If this is present in the documentation or vignettes, let me know and I will fix it!

This uses the interaction types as shown by categoriseInteractions(), so you can always use that function to check what the interaction types are called. You can also use GenomicInteractions::availableDisplayPars to check which other displayPars you can set.

Hope you're finding the package helpful!

Hi Marco,

There is a typo in the name of the display parameter you're setting - it should be col.interaction.types. If this is present in the documentation or vignettes, let me know and I will fix it!

This uses the interaction types as shown by categoriseInteractions(), so you can always use that function to check what the interaction types are called. You can also use GenomicInteractions::availableDisplayPars to check which other displayPars you can set.

Hope you're finding the package helpful!