ixxmu
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1 year ago R优雅的自定义绘制代谢通路图 by 生信宝库
❝最近看到一个非常好的案例来分享一下，使用igraph，ggraph等R包来自定义绘制代谢通路pathway，原文文档链接见下方，数据可自行去官网下载。代码过程很是简洁，当然难点也许在于构建边文件与点文件。这需要各位观众老爷细细品味
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原文文档
❝https://github.com/cxli233/ggpathway
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淘宝店铺个性化绘图服务
❝最近有部分观众老爷找小编做个性化绘图，为了给观众老爷提供更加优质的服务；小编开通了 「淘宝店铺(R语言数据分析指南)」 ，有特殊绘图需求的欢迎关注咨询(「由于小编时间精力有限有需求的请及时下单」)
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加载R包
library(tidyverse)
library(igraph)
library(ggraph)
library(readxl)
library(viridis)
library(RColorBrewer)
library(rcartocolor)
构建边数据
example1_edge_table <- tribble(
~from, ~to, ~label,
"Glc6P", "6P-gluconolactone", "Glc6PHD",
"6P-gluconolactone", "6P-glucoconate", "6P-gluconolactonase",
"6P-glucoconate", "Ru5P", "6P-gluconateDH"
)
# 构建点数据
example1_nodes_table <- tribble(
~name, ~x, ~y,
"Glc6P", 1, 0,
"6P-gluconolactone", 2, 0,
"6P-glucoconate", 3, 0,
"Ru5P", 4, 0
)
文件整合
example1_network <- graph_from_data_frame(
d = example1_edge_table,
vertices = example1_nodes_table,
directed = T
)
绘制基础通路图
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()
绘制PPP代谢途径
导入数据
example2_edges <- read_excel("OPPP_edges.xlsx")
example2_nodes <- read_excel("OPPP_nodes.xlsx")
构建新标签
example2_nodes <- example2_nodes %>%
mutate(label = str_remove(name, "_\\d"))
文件整合
example2_network <- graph_from_data_frame(
d = example2_edges,
vertices = example2_nodes,
directed = T)
绘制PPP代谢途径图
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(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()
TCA途径
导入数据
example3_edges <- read_excel("TCA_cycle_edges.xlsx")
example3_nodes <- read_excel("TCA_cycle_nodes.xlsx")
构建标签文本
example3_nodes <- example3_nodes %>%
mutate(label = str_remove(name, "_\\d"))
整合数据
example3_network <- graph_from_data_frame(
d = example3_edges,
vertices = example3_nodes,
directed = T)
绘制TCA途径图
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 = "black") +
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()
❝好了本节介绍到此结束，整个代码还是非常简洁的，
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