R语言学习推荐网站 | 值得收藏

2023-07-16 本文已影响0人小杜的生信筆記

写在前面

我们一直在推R绘制的基础教程，一是书籍的推荐，二是学习代码的推荐。在现在啥啥都可以“度娘”的时代，网络资源真的很多。我们在网络上基本可以查到自己想要的内容（PS：只要你想查）。今天也推荐小杜自己收藏的一个使用R语言绘图的网址：The R Graph Gallery.

教程网址

https://r-graph-gallery.com/

网站内容

里面包含了很多图形的绘制基础代码，基本可以根据代码直接出图，很是方便。

每个图形你点击进去后，就会出现这个图形的绘制代码。

操作例子

点击Edge bundling
进去后也有不同的选项
点击你想要的图形，显示绘图代码

绘图代码

加载数据

#'@加载数据
library(ggraph)
library(igraph)
library(tidyverse)

##'@创建数据框架
set.seed(1234)
d1 <- data.frame(from="origin", to=paste("group", seq(1,10), sep=""))
d2 <- data.frame(from=rep(d1$to, each=10), to=paste("subgroup", seq(1,100), sep="_"))
hierarchy <- rbind(d1, d2)
head(hierarchy)

##'@创建数据
all_leaves <- paste("subgroup", seq(1,100), sep="_")
connect <- rbind( 
  data.frame( from=sample(all_leaves, 100, replace=T) , to=sample(all_leaves, 100, replace=T)), 
  data.frame( from=sample(head(all_leaves), 30, replace=T) , to=sample( tail(all_leaves), 30, replace=T)), 
  data.frame( from=sample(all_leaves[25:30], 30, replace=T) , to=sample( all_leaves[55:60], 30, replace=T)), 
  data.frame( from=sample(all_leaves[75:80], 30, replace=T) , to=sample( all_leaves[55:60], 30, replace=T)) )
connect$value <- runif(nrow(connect))

# create a vertices data.frame. One line per object of our hierarchy
vertices  <-  data.frame(
  name = unique(c(as.character(hierarchy$from), as.character(hierarchy$to))) , 
  value = runif(111)
) 
#'@添加分组
vertices$group  <-  hierarchy$from[ match( vertices$name, hierarchy$to ) ]

# Create a graph object
mygraph <- graph_from_data_frame( hierarchy, vertices=vertices )

# The connection object must refer to the ids of the leaves:
from  <-  match( connect$from, vertices$name)
to  <-  match( connect$to, vertices$name)

数据
绘制基础图形

##'@绘制基础图形
ggraph(mygraph, layout = 'dendrogram', circular = TRUE) + 
  geom_conn_bundle(data = get_con(from = from, to = to), alpha=0.2, colour="skyblue", tension = .5) + 
  geom_node_point(aes(filter = leaf, x = x*1.05, y=y*1.05)) +
  theme_void()

美化图形

给了几种美化图形的方案，你可以作为参考进行修改。我们这里就不统一罗列出来。

p <- ggraph(mygraph, layout = 'dendrogram', circular = TRUE) + 
  geom_node_point(aes(filter = leaf, x = x*1.05, y=y*1.05)) +
  theme_void()

# 0.1
p +  geom_conn_bundle(data = get_con(from = from, to = to), alpha=0.2, colour="skyblue", width=0.9, 
                      tension=0.1)

颜色参数

# Use the 'value' column of the connection data frame for the color:
p +  geom_conn_bundle(data = get_con(from = from, to = to), aes(colour=value, alpha=value))

p +  
  geom_conn_bundle(data = get_con(from = from, to = to), width=1, alpha=0.2, aes(colour=..index..)) +
  scale_edge_colour_distiller(palette = "RdPu") +
  theme(legend.position = "none")
ggsave("color02.pdf",width = 6, height = 6)