KEGG通路图绘制 | ggpathway包

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写在前面

今天在GitHub中看到一个ggpathway的包，主要可以制作通路网络图，或是进一步优化的话，可以进行个性话制作。操作步骤在GitHub中已经很详细。自己也照葫芦画瓢进行运行一下。

GitHub网址：https://github.com/cxli233/ggpathway
**「获得本教程代码链接：」**任意赞赏即可获得

绘图

1，导入所需R包

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library(tidyverse)
library(igraph)
library(ggraph)

library(readxl)

library(viridis)
library(RColorBrewer)
#BiocManager::install("rcartocolor")
library(rcartocolor)

exaple one

创建数据

Edge table

example1_edge_table <- tribble(
~from, ~to, ~label,
"Glc6P", "6P-gluconolactone", "Glc6PHD",
"6P-gluconolactone", "6P-glucoconate", "6P-gluconolactonase",
"6P-glucoconate", "Ru5P", "6P-gluconateDH"
)

head(example1_edge_table)

A tibble: 3 × 3

from to label
<chr> <chr> <chr>
1 Glc6P 6P-gluconolactone Glc6PHD
2 6P-gluconolactone 6P-glucoconate 6P-gluconolactonase
3 6P-glucoconate Ru5P 6P-gluconateDH

Node table

example1_nodes_table <- tribble(
~name, ~x, ~y,
"Glc6P", 1, 0,
"6P-gluconolactone", 2, 0,
"6P-glucoconate", 3, 0,
"Ru5P", 4, 0
)

Make network object and graph

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## Make network object and graph
example1_network <- graph_from_data_frame(
  d = example1_edge_table,
  vertices = example1_nodes_table,
  directed = T
)

head(example1_nodes_table)

> head(example1_nodes_table)
# A tibble: 4 × 3
  name                  x     y
  <chr>             <dbl> <dbl>
1 Glc6P                 1     0
2 6P-gluconolactone     2     0
3 6P-glucoconate        3     0
4 Ru5P                  4     0

绘图

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ggraph(example1_network, layout = "manual", 
       x = x, y = y) +
  geom_node_text(aes(label = name), hjust = 0.5) +
  geom_edge_link(aes(label = example1_edge_table$label), 
                 angle_calc = 'along',
                 label_dodge = unit(2, 'lines'),
                 arrow = arrow(length = unit(0.5, 'lines')), 
                 start_cap = circle(4, 'lines'),
                 end_cap = circle(4, 'lines')) +
  theme_void()  

ggsave("../Results/Pentose_1.svg", height = 2, width = 6.5, bg = "white")
ggsave("../Results/Pentose_1.png", height = 2, width = 6.5, bg = "white")

Example 2: more complex pathway

导入所需数据

setwd("E:\小杜的生信筆記\2023\20231022_ggpathway")
##'@input data
example2_edges <- read_excel("Data/OPPP_edges.xlsx")
example2_nodes <- read_excel("Data/OPPP_nodes.xlsx")

head(example2_edges)

A tibble: 6 × 3

from to label
<chr> <chr> <chr>
1 Glc6P 6P-gluconolactone Glc6PHD
2 6P-gluconolactone 6P-glucoconate 6P-gluconolactonase
3 6P-glucoconate Ru5P 6P-gluconateDH
4 Ru5P R5P R5P isomerase
5 Ru5P Xu5P_1 R5P epimerase
6 Xu5P_1 R5P T

head(example2_nodes)

A tibble: 6 × 5

name x y carbons label
<chr> <dbl> <dbl> <dbl> <chr>
1 Glc6P 0 0 6 Glc6P
2 6P-gluconolactone 0 -1 6 6P-gluconolactone
3 6P-glucoconate 0 -2 6 6P-glucoconate
4 Ru5P 0 -3 5 Ru5P
5 R5P -0.5 -4 5 R5P
6 Xu5P_1 0 -4 5 Xu5P
计算 nodes

example2_nodes <- example2_nodes %>%
mutate(label = str_remove(name, "_\d"))

head(example2_nodes)

A tibble: 6 × 5

name x y carbons label
<chr> <dbl> <dbl> <dbl> <chr>
1 Glc6P 0 0 6 Glc6P
2 6P-gluconolactone 0 -1 6 6P-gluconolactone
3 6P-glucoconate 0 -2 6 6P-glucoconate
4 Ru5P 0 -3 5 Ru5P
5 R5P -0.5 -4 5 R5P
6 Xu5P_1 0 -4 5 Xu5P

example2_network <- graph_from_data_frame(
d = example2_edges,
vertices = example2_nodes,
directed = T
)
绘图

ggraph(example2_network, layout = "kk") +
geom_node_point(size = 3, aes(fill = as.factor(carbons)),
alpha = 0.8, shape = 21, color = "grey20") +
geom_node_text(aes(label = label), hjust = 0.5, repel = T) +
geom_edge_link(#aes(label = example2_edges$label),
#angle_calc = 'along',
label_dodge = unit(2, 'lines'),
arrow = arrow(length = unit(0.4, 'lines')),
start_cap = circle(1, 'lines'),
end_cap = circle(2, 'lines')) +
scale_fill_manual(values = carto_pal(7, "Vivid")) +
labs(fill = "Carbons") +
theme_void()

ggsave("Results/Pentose_2.svg", height = 5, width = 4, bg = "white")
ggsave("Results/Pentose_2.png", height = 5, width = 4, bg = "white")

Example 3: circular pathway

导入数据和数据转换

example3_edges <- read_excel("Data/TCA_cycle_edges.xlsx")
example3_nodes <- read_excel("Data/TCA_cycle_nodes.xlsx")

head(example3_edges)
head(example3_nodes)

example3_nodes <- example3_nodes %>%
mutate(label = str_remove(name, "_\d"))

head(example3_nodes)

example3_network <- graph_from_data_frame(
d = example3_edges,
vertices = example3_nodes,
directed = T
)
绘图

ggraph(example3_network, layout = "manual",
x = x, y = y) +
geom_node_point(size = 3, aes(fill = as.factor(carbons)),
alpha = 0.8, shape = 21, color = "grey20") +
geom_edge_link(arrow = arrow(length = unit(0.4, 'lines')),
start_cap = circle(0.5, 'lines'),
end_cap = circle(0.5, 'lines'),
width = 1.1, alpha = 0.5) +
geom_node_text(aes(label = label), hjust = 0.5, repel = T) +
annotate(geom = "text", label = "TCA Cycle",
x = 0, y = 0, size = 5, fontface = "bold") +
scale_fill_manual(values = carto_pal(7, "Vivid")) +
labs(fill = "Carbons") +
theme_void() +
coord_fixed()

Subsetting pathway

数据和计算转换

example3_nodes_trim <- example3_nodes %>%
filter(carbons != "cofactor")

example3_edges_trim <- example3_edges %>%
filter(from %in% example3_nodes_trim $name & to %in% example3_nodes_trim$ name)

example3_network_trim <- graph_from_data_frame(
d = example3_edges_trim,
vertices = example3_nodes_trim,
directed = T
)

绘图

复制代码

ggraph(example3_network_trim, layout = "manual",
       x = x, y = y) +
  geom_node_point(size = 3, aes(fill = as.factor(carbons)), 
                  alpha = 0.8, shape = 21, color = "grey20") +
  geom_edge_link(arrow = arrow(length = unit(0.4, 'lines')), 
                 start_cap = circle(0.5, 'lines'),
                 end_cap = circle(1, 'lines'), 
                 width = 1.1, alpha = 0.5) +
  geom_node_text(aes(label = label), hjust = 0.5, repel = T) +
  annotate(geom = "text", label = "TCA Cycle", 
           x = 0, y = 0, size = 5, fontface = "bold") +
  scale_fill_manual(values = carto_pal(7, "Vivid")) +
  labs(fill = "Carbons") +
  theme_void() +
  coord_fixed()

ggsave("Results/TCA_2.svg", height = 4, width = 5, bg = "white")
ggsave("Results/TCA_2.png", height = 4, width = 5, bg = "white")