highlight_entities function may cause elements to be omitted and element misalignment

[BioLaoXu]

dear ggkegg team，Thanks to ggkegg for providing a more flexible KEGG pathway visualization scheme,But I found some minor problems in the process of using it, which may be caused by my own misunderstanding.

• highlight_entities function may cause elements omit，After looking at the contents of the xml, I found that some genes have a '...' at the end, highlight_entities function and highlight_set_nodes function do not remove this character.

hsn=c("K01568","D18Wsu181e")
g <- pathway("mmu00010",group_rect_nudge=0)
g <- g |> mutate(gene1=highlight_set_nodes(hsn,sep=" ",how="any",name="name"),
                 gene2=highlight_set_nodes(hsn,sep=", ",how="any",name="graphics_name"))
gg=ggraph(g, layout="manual", x=x, y=y)
gg+
  overlay_raw_map()+
  geom_node_rect(fill="red",aes(filter=gene1), color="black")+
  geom_node_text(aes(
    label=graphics_name %>% strsplit(",") %>% sapply("[", 1) %>% strsplit("\\.") %>% sapply("[", 1),
    filter=gene1),size=2)+
  geom_node_rect(fill="red",aes(filter=gene2), color="black")+
  geom_node_text(aes(
    label=graphics_name %>% strsplit(",") %>% sapply("[", 1) %>% strsplit("\\.") %>% sapply("[", 1),
    filter=gene2),size=2)+
  theme_void()

#ggkegg::highlight_entities(pathway = "mmu00010",set = hsn,how = "any",name ="graphics_name" ) ## not work

in this example,D18Wsu181egene will be oimted

• element misalignment,I want to add the text more personalized，this is my solution:

highlight_entities_dt=data.frame(showtext=c("P52792","Q9DBF1","P15327","P52792","Q9DBF1"),
                                 lfc=c(-2,2,4,6,8),
                                 # symbol=c("1","2","2","Akr1a1","K00138")
                                 symbol=c("P52792","Q9DBF1","Bpgm","Gck","Aldh7a1")
                                 )

pid="mmu00010"
showText="showtext"
colorBy="lfc"

g <- pathway(pid,group_rect_nudge=0,directory = getBFCOption("CACHE"))
gg=ggraph(g, layout="manual", x=x, y=y)
gt=gg$data

tmp=gt%>%mutate(idx = row_number())
gt1=tmp%>%separate_rows(.,graphics_name, convert = TRUE,sep = ", ")%>%
  mutate(symbol=gsub(" ","",graphics_name)%>%gsub("\\.\\.\\.$","",.))
gt2=tmp%>%separate_rows(.,name, convert = TRUE,sep = " ")%>%
  mutate(symbol=gsub(" ","",name)%>%gsub("\\.\\.\\.$","",.))
gt1=left_join(gt1,highlight_entities_dt,by="symbol")%>%
  mutate(sn=get(showText)%>%lapply(.,function(x){
    if(x%in%highlight_entities_dt[[showText]]){
      return(x)
    }
    return(NA)
  })%>%unlist())%>%
  .[with(., order(idx,sn,symbol,decreasing = F)),]
gt2=left_join(gt2,highlight_entities_dt,by="symbol")%>%
  mutate(sn=get(showText)%>%lapply(.,function(x){
    if(x%in%highlight_entities_dt[[showText]]){
      return(x)
    }
    return(NA)
  })%>%unlist())%>%
  .[with(., order(idx,sn,symbol,decreasing = F)),]
gt12=rbind(gt1,gt2)%>% 
  distinct(.,idx,.keep_all = T)
gt12$name=gt$name
gt12$graphics_name=gt$graphics_name
gt=gt12

g=pathway(pid,group_rect_nudge=0,directory = getBFCOption("CACHE")) %>% 
  mutate(sn = gt[[showText]],!!colorBy:=gt[[colorBy]])
### method1,more tidy graph
ggraph(g, layout = "manual",x=x,y=y)+
  overlay_raw_map(high_res=F, transparent_color="#FFFFFF")+
  geom_node_rect(aes(filter=!is.na(sn),fill=.data[[colorBy]]), color="black")+
  scale_fill_gradientn(name=colorBy,colours = scales::alpha(c("#3288BD","#D53E4F"),alpha = .99),
                        space = "lab",
                        breaks=ceiling(seq(min(gt[[colorBy]],na.rm = T),max(gt[[colorBy]],na.rm = T),
                                           (max(gt[[colorBy]],na.rm = T)-min(gt[[colorBy]],na.rm = T))/4)),
                        guide = guide_colorbar(order = 3))+
  geom_node_text(aes(filter=!is.na(sn),label=sn), size=2)+
  theme_void()

### method2
ggraph(g, layout =gt,x=x,y=y)+
  overlay_raw_map(high_res=F, transparent_color="#FFFFFF")+
  geom_node_rect(aes(filter=!is.na(sn),fill=.data[[colorBy]]), color="black")+
  scale_fill_gradientn(name=colorBy,colours = scales::alpha(c("#3288BD","#D53E4F"),alpha = .99),
                        space = "lab",
                        breaks=ceiling(seq(min(gt[[colorBy]],na.rm = T),max(gt[[colorBy]],na.rm = T),
                                           (max(gt[[colorBy]],na.rm = T)-min(gt[[colorBy]],na.rm = T))/4)),
                        guide = guide_colorbar(order = 3))+
  geom_node_text(aes(filter=!is.na(sn),label=sn), size=2)+
  theme_void()

With the exception of the misalignment of the elements, the results were as expected

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocFileCache_2.4.0 dbplyr_2.2.1        tidyr_1.3.0         ggkegg_1.3.1        XML_3.99-0.14       ggraph_2.1.0       
 [7] ggplot2_3.4.2       igraph_2.0.3        dplyr_1.1.2         tidygraph_1.2.2    

look forward to hearing from you,thanks

[noriakis]

Thank you very much for raising this important point. For point 1, I have implemented the remove_dot option in highlight_entities and highlight_set_nodes now and it should handle the gene names with dots after them (devel and main branches). I will go through point 2 next but thanks again for using the package.