Mengqingyao

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Introduction

KEGG pathway and module correspondence information. Click

Data preparation

  • tools_RStudio_result_all
  • Maps_Moules_2023_11_16
  • tools_RStudio_映射模块上的K号

R script for tree + heatmap

#!/usr/bin/env Rscript
# -*- coding: utf-8 -*-
# @Author    : mengqingyao
# @Time      : 20231116

library(readr)
library(tidyfst)

tools_RStudio_result_all <- read_delim("tools_RStudio_result_all.txt", 
                                       delim = "\t", escape_double = FALSE, 
                                       trim_ws = TRUE)

Maps_Moules_2023_11_16 <- read_delim("F:/database/KEGG/KEGG_General_Documentation_module/Maps_Moules_2023_11_16.txt", 
                                     delim = "\t", escape_double = FALSE, 
                                     col_names = FALSE, trim_ws = TRUE)

tools_RStudio_映射模块上的K号 <- read_delim("tools_RStudio_映射模块上的K号.txt", 
                                     delim = "\t", escape_double = FALSE, 
                                     col_names = FALSE, trim_ws = TRUE)


map01230 <- Maps_Moules_2023_11_16 %>% filter_dt(X2 == "map01230")
map01230 <- map01230 %>% rename_dt(m_id = X1)
map01230_1 <- map01230 %>% inner_join_dt(tools_RStudio_result_all,by = "m_id")
write.table(map01230_1,file = "map01230.txt",sep = "\t",quote = F,row.names = F)
  • map01230.txt
#!/usr/bin/env Rscript
# -*- coding: utf-8 -*-
# @Author    : mengqingyao
# @Time      : 20231118

library(ggtree)
library(ggtreeExtra)
library(tidyfst)

map01230 <- read_delim("map01230.txt", delim = "\t", 
                       escape_double = FALSE, trim_ws = TRUE)

map01230 <- map01230 %>% select(-X2)

head_data <- map01230 %>% longer_dt(name = "species",value = "complet")

a <- map01230 %>% column_to_rownames(var="m_name")

tree <- map01230 %>% column_to_rownames(var="m_name") %>%
  #  该函数使用指定的距离度量计算数据矩阵行间的距离，计算并返回距离矩阵。
  dist() %>% 
  #  Tree Estimation Based on an Improved Version of the NJ Algorithm
  ape::bionj()

ggtree(tree,branch.length = "none", layout = "circular",
       linetype = 1,size = 0.5, ladderize = T)+
  layout_fan(angle =180)+ # 调整开口
  geom_tiplab(offset=11,show.legend=FALSE,size=2,
              color = "black",starstroke = 0)+
  geom_fruit(data=head_data,
                       geom=geom_tile,
                       mapping=aes(y=m_name,x=species,fill=complet),
                       pwidth=0.8,
                       offset=0.04,
                       color = "white",
                       axis.params=list(axis="x",text.angle=-90,text.size=1,hjust=0))+
  scale_fill_gradientn(colours = RColorBrewer::brewer.pal(100,"Blues")) +
  theme(plot.margin=margin(8,-6,0,0,"cm"),# 上下,左右,远近
        legend.position = c(1.3,0.8),
        legend.background = element_rect(fill = NA), 
        )

Rsudio is recommended for running this script.

I wrote this script a long time ago, and there is a lot of redundant code, but this is the original processing logic.

It's better to understand.

Result

Beautification

  1. I would suggest saving the image as a pdf.
  2. Evolutionary landscaping using Adobe Illustrator.
  3. Save images as needed.

Quote

Email me with more questions! 584338215@qq.com

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