noriakis
commented
5 months ago Hi @Ramirj, I cannot replicate the issue as I don't have LFC vector. Please provide a reproducible example (consult here for instance). In general, you should double-check whether the value is available in the tbl_graph.
Hi @noriakis,
I'm making pathway diagrams for the Lysine Biosynthesis pathway using ggkegg, but for some reason the mapping between reaction numbers and ec numbers doesn't work for some nodes. For example, one reaction number that I'm trying to map is "rn:R04199", but when I run my code the corresponding node doesn't get highlighted. However, when I try other reaction numbers it works fine so I'm confused what the issue is.
I'm using this link to map RN to EC numbers: https://rest.kegg.jp/link/reaction/ec I checked and the link has the rn to ec conversion in it so it should work. Do you know what could be causing the issue?
Here's my code:
Load libraries
library(ggkegg) library(BiocFileCache) library(viridis)
Fetch and cache RN to EC map
url <- "https://rest.kegg.jp/link/reaction/ec" bfc <- BiocFileCache() path <- bfcrpath(bfc, url) convert <- data.frame(data.table::fread(path, header = FALSE, sep = "\t")) rntoec <- convert$V1 |> strsplit(":") |> vapply("[", 2, FUN.VALUE = "a") |> setNames(convert$V2)
Define the pathway ID
pathway_id <- "dosa00300" # Change depending on the pathway you want to map
Create a graph of the pathway
g <- pathway(pathway_id) |> mutate(ec = rntoec[reaction])
Define a vector of node names to highlight
nodes_to_highlight <- reaction
Add log fold changes (LFCs) to the graph
LFC_vector <- LFCs # Make sure LFCs is a vector with values for each corresponding reaction number
g <- g %>% mutate( LFC = ifelse(reaction %in% nodes_to_highlight, LFC_vector, NA), Color = ifelse(LFC <= -1, "red", ifelse(LFC >= 1, "green", NA)) # red for repressed genes and green for induced genes )
Create a pathway diagram with colors to visualize LFCs
gg <- g |> filter(type %in% c("compound", "gene")) |> ggraph(layout = "manual", x = x, y = y) + geom_node_rect(aes(fill = Color), size = 5) + # Use Color for the fill aesthetic scale_fill_identity() + # Use identity scale for custom colors overlay_raw_map("dosa00300") + # Make diagram look better (change depending on pathway you're mapping) theme_minimal() + # Set background to white theme_void() + # Remove x and y axis ggtitle("Induced (Green) and Repressed (Red) Genes in Lysine Biosythesis Pathway - 0 hr Timepoint")
gg