noriakis
commented
7 months ago Hi, highlight_set_nodes searches for the name column in node data by default as described in the manual. You should change name argument to reaction if you search for the reaction column, like:
highlight_set_nodes(highlight_reaction, name="reaction", how="all")I think raising the warning or the message could be useful if none of the nodes is highlighted. I will update the feature in dev.
Hi @noriakis,
I'm trying to highlight specific gene nodes on raw KEGG maps using ggkegg but for some reason it isn't working for me. Is it possible to achieve this using this package? This is the code that I tried to use:
reaction <- c("rn:R00756") g <- pathway("dosa00010") |> mutate(mod=highlight_set_nodes(reaction, how="all")) ggraph(g, layout="manual", x=x, y=y)+ geom_node_rect(fill="grey",aes(filter=type == "ortholog"))+ overlay_raw_map("dosa00010")+ geom_node_point(aes(filter=type == "reaction"), shape=21, fill="blue", color="black", size=2)+ ggfx::with_outer_glow( geom_node_point(aes(filter=mod, x=x, y=y), color="red",size=2), colour="yellow",expand=5 )+ theme_void()
And this is the resulting plot:
I didn't receive any error messages or anything, but the gene node that I wanted to highlight was not highlighted. If you could provide some insight that would be great. Thank you!