生信技能树 Day6 R语言作图入门

#1.基础包 略显陈旧 了解一下一般不用
plot(iris[,1],iris[,3],col = iris[,5]) 
text(6.5,4, labels = 'hello') # 图例的位置

dev.off() #关闭画板

#2.ggplot2 中坚力量，语法有个性，扩展性强，推荐使用
library(ggplot2)
ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species))

#3.ggpubr 新手友好型 ggplot2简化和美化 褒贬不一
library(ggpubr)
ggscatter(iris,
          x="Sepal.Length",
          y="Petal.Length",
          color="Species")

ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length))

# 作图数据 作什么图 xy轴
# 特殊语法：列名不带引号，行末写加号按回车自动缩进

#2.1 手动设置，需要设置为有意义的值

ggplot(data = iris) + 
  geom_point(mapping = aes(x = Sepal.Length, # mapping映射
                           y = Petal.Length), 
             color = "blue")

ggplot(data = iris) + 
  geom_point(mapping = aes(x = Sepal.Length, y = Petal.Length), 
             size = 5,     # 点的大小5mm
             alpha = 0.5,  # 透明度 50%
             shape = 8)  # 点的形状

#2.2 映射：按照数据框的某一列来定义图的某个属性
ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species))

## 映射color：根据某一列的内容分配颜色。手动设置：把图形设置为一或多个颜色，与数据内容无关

## Q1 能不能自行指定映射的具体颜色？注意写加号 映射和指定颜色必须都要写 十六进制颜色编码

ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species))+
  scale_color_manual(values = c("blue","grey","red"))

# 好用的配色R包 RColorBrewer ggsci paletteer
ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species))+
  scale_color_brewer(palette = "Set1")

## Q2 区分color和fill两个属性
### Q2-1 空心形状和实心形状都用color设置颜色
ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species),
             shape = 17) #17号，实心的例子

ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species),
             shape = 2) #2号，空心的例子

### Q2-2 既有边框又有内心的，才需要color和fill两个参数

ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species),
             shape = 24,
             fill = "black") #24号，双色的例子

# geom_开头的函数是画图函数，画出的是一个几何对象，一个图层，图层可以叠加
#局部设置和全局设置
## 局部设置
ggplot(data = iris) + 
  geom_smooth(mapping = aes(x = Sepal.Length, 
                          y = Petal.Length))+
  geom_point(mapping = aes(x = Sepal.Length, 
                           y = Petal.Length))

## 全局设置 每个图层有特殊设置的地方可以单独写在他的括号里
ggplot(data = iris,mapping = aes(x = Sepal.Length, y = Petal.Length))+
  geom_smooth()+
  geom_point()

ggplot(data = iris,mapping = aes(x = Species, y = Sepal.Width, fill = Species))+
  geom_boxplot()+
  geom_point()

# 发现点图的所有点都在一条竖线上，存在很多重叠的点，失真
## 抖动的点图
ggplot(data = iris,mapping = aes(x = Species, 
                                 y = Sepal.Width,
                                 fill = Species)) + 
  geom_boxplot()+
  #geom_point(position = "jitter")
  geom_jitter()

ggplot(data = iris,mapping = aes(x = Species, 
                                 y = Sepal.Width,
                                 fill = Species)) + 
  geom_boxplot()+
  geom_jitter()+ 
  coord_flip() ## 翻转坐标系

ggplot(data = iris,mapping = aes(x = Species, 
                                 y = Sepal.Width,
                                 fill = Species)) + 
  geom_boxplot()+
  geom_jitter()+ 
  theme_bw() ## 改主题，去掉灰色格子 theme_函数

ggplot(data = iris,mapping = aes(x = Sepal.Width, y = Species))+
  geom_violin(aes(fill = Species))+
  geom_boxplot()+
  geom_jitter(aes(shape = Species))
  # 图层顺序与代码顺序有关

# ggpubr 搜代码直接用，基本不需要系统学习

# sthda上有大量ggpubr出的图
library(ggpubr)
p = ggboxplot(iris, x = "Species", y = "Sepal.Length",
              color = "Species", shape = "Species",add = "jitter") # 代码很简单
p

# 添加显著性标记
my_comparisons <- list( c("setosa", "versicolor"), 
                        c("setosa", "virginica"), 
                        c("versicolor", "virginica") )# list打包向量
p + stat_compare_means(comparisons = my_comparisons,
                       aes(label = after_stat(p.signif)))

#图片保存的三种方法
#1.基础包作图的保存
pdf("iris_box_ggpubr.pdf")
boxplot(iris[,1]~iris[,5])
text(6.5,4, labels = 'hello')
dev.off() # 关闭画板，不出图可能是没关闭画板

#2.ggplot系列图(包括ggpubr)通用的简便保存 ggsave
p <- ggboxplot(iris, x = "Species", 
               y = "Sepal.Length",
               color = "Species", 
               shape = "Species",
               add = "jitter")
ggsave(p,filename = "iris_box_ggpubr.png")

#3.eoffice包 导出为ppt,全部元素都是可编辑模式
library(eoffice)
topptx(p,"iris_box_ggpubr.pptx")