zjyzjjzmt/ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

ggkegg

A set of functions to analyse and plot the KEGG information using tidygraph, ggraph and ggplot2.

The detailed documentation is here using bookdown.

Installation

Using BiocManager:

BiocManager::install("ggkegg")

Using devtools:

devtools::install_github("noriakis/ggkegg")

Examples

library(ggkegg)
library(ggfx)
library(igraph)
library(tidygraph)
library(dplyr)

pathway("ko01100") |>
  process_line() |>
  highlight_module(module("M00021")) |>
  highlight_module(module("M00338")) |>
  ggraph(x=x, y=y) +
  geom_node_point(size=1, aes(color=I(fgcolor),
                              filter=fgcolor!="none" & type!="line"))+
  geom_edge_link0(width=0.1, aes(color=I(fgcolor),
                                filter=type=="line"& fgcolor!="none"))+
  with_outer_glow(
    geom_edge_link0(width=1,
                   aes(color=I(fgcolor),
                       filter=(M00021 | M00338))),
    colour="red", expand=5
  )+
  with_outer_glow(
    geom_node_point(size=1.5,
                    aes(color=I(fgcolor),
                        filter=(M00021 | M00338))),
    colour="red", expand=5
  )+
  geom_node_text(size=2,
                 aes(x=x, y=y,
                     label=graphics_name,
                     filter=name=="path:ko00270"),
                 repel=TRUE, family="sans", bg.colour="white")+
  theme_void()

You can use your favorite geoms to annotate raw KEGG map combining the functions.

m <- module("M00013")
g <- pathway("ko00640") |> mutate(mod=highlight_set_nodes(m@reaction_components,how="all"))
gg <- ggraph(g, layout="manual", x=x, y=y)+
  geom_node_rect(fill="grey",aes(filter=type=="ortholog"))+
  overlay_raw_map("ko00640")+
  geom_node_point(aes(filter=type=="compound"), 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()
gg

Or customize graphics based on ggraph.

g <- pathway("hsa04110")
pseudo_lfc <- sample(seq(0,3,0.1), length(V(g)), replace=TRUE)
names(pseudo_lfc) <- V(g)$name

ggkegg("hsa04110",
       convert_org = c("pathway","hsa","ko"),
       numeric_attribute = pseudo_lfc)+
  geom_edge_parallel2(
    aes(color=subtype_name),
    arrow = arrow(length = unit(1, 'mm')), 
    start_cap = square(1, 'cm'),
    end_cap = square(1.5, 'cm')) + 
  geom_node_rect(aes(filter=.data$type=="group"),
                 fill="transparent", color="red")+
  geom_node_rect(aes(fill=numeric_attribute,
                     filter=.data$type=="gene"))+
  geom_node_text(aes(label=converted_name,
                     filter=.data$type == "gene"),
                 size=2.5,
                 color="black")+
  with_outer_glow(geom_node_text(aes(label=converted_name,
                                     filter=converted_name=="PCNA"),
                                 size=2.5, color="red"),
                  colour="white",
                  expand=4)+
  scale_edge_color_manual(values=viridis::plasma(11))+
  scale_fill_viridis(name="LFC")+
  theme_void()