1.R语言安装

官网下载windows版本

2.Rstudio安装

官网下载windows版本

3.外观设置

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4.学习作图：

1.散点图

plot(rnorm(50))

散点图

2.箱线图

boxplot(iris$Sepal.Length~iris$Species,col = c("lightblue","lightyellow","lightpink"))

箱线图

3.热图

安装加载pheatmap

install.packages("pheatmap")
library(pheatmap)

创建一个矩阵，设置行名为Gene1-20和列名Test1-10

test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")

创建矩阵

画图

pheatmap(test)

画图

设置kmean数值

pheatmap(test, kmeans_k = 2)

设置kmean数值

进行归一化

pheatmap(test, scale = "row", clustering_distance_rows = "correlation")

进行归一化

修改颜色

pheatmap(test, color = colorRampPalette(c("navy", "white", "firebrick3"))(50))

修改颜色

修改行或者列聚类

pheatmap(test, cluster_row = FALSE)

修改行或者列聚类

设置图像长宽

pheatmap(test, cellwidth = 15, cellheight = 12, main = "Example heatmap")

设置图像长宽

添加注释

annotation_col = data.frame( CellType = factor(rep(c("CT1", "CT2"), 5)), Time = 1:5)
rownames(annotation_col) = paste("Test", 1:10, sep = "")
annotation_row = data.frame(  GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6)))) 
rownames(annotation_row) = paste("Gene", 1:20, sep = "")
pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row)

添加注释

修改行文本角度

pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row, angle_col = "45")

修改行文本角度

分裂行或列

pheatmap(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14), cutree_col = 2)

分裂行或列

添加想要的行名

labels_row = c("", "", "", "", "", "", "", "", "", "", "", "", "", "", "","", "", "Il10", "Il15", "Il1b")
pheatmap(test, annotation_col = annotation_col, labels_row = labels_row)

添加想要的行名

5.基本操作：

R project 管理工作目录

getwd() #查看工作目录
setwd() #设置工作目录

新建一个R project

新建
新建成功

显示文件列表

> dir()
[1] "Test.Rproj"
>list.files()
[1] "Test.Rproj"

简单运算

> 1+5
[1] 6

赋值

> a<-666
> a
[1] 666

删除变量

rm(list=ls()) #清空所有变量

历史命令

history()

history()

清空控制台

Ctrl+l