day5记录 R语言绘图

plot(iris[,1],iris[,3],col = iris[,5]) 
text(6.5,4, labels = 'hello')
dev.off() #关闭画板

library(ggplot2)
ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species))

library(ggpubr)
ggscatter(iris,
          x="Sepal.Length",
          y="Petal.Length",
          color="Species")

library(ggplot2)

ggplot(data = iris)+
  geom_point(mapping = aes(x = iris[,1],
                           y = Petal.Length))

ggplot(data = iris) + 
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length), 
             color = "red",
             alpha = 0.4,
             shape = iris[,4])

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

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

ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species))+
  scale_color_manual(values = c("blue","grey","red")) #删除color=Species，这行代码无法改变颜色

ggplot(data = iris)+
  geom_point(mapping = aes(x = Sepal.Length,
                           y = Petal.Length,
                           color = Species))+
  scale_color_manual(values = c("#2874C5","#e6b707","#f87669"))

if(!require(paletteer))install.packages("paletteer",ask = F,update = F)
if(!require(awtools))install.packages("awtools",ask = F,update = F)
library(paletteer)
ggplot(data = iris)+ 
  geom_point(mapping = aes(x = Sepal.Length, 
                           y = Petal.Length, 
                           color = Species))+ 
  scale_color_paletteer_d("awtools::mpalette")  #用别人R包里的配色
palettes_d_names
#View(palettes_d_names)

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),
             shape = 24,
             color = "red",          				     
             fill = "yellow") #24号，双色的例子 fill：里面填充的颜色 color：可能是实心也可能是空心

ggplot(data = iris) + 
  geom_smooth(mapping = aes(x = Sepal.Length, 
                          y = Petal.Length))+ #此处为局部设置 仅对当前图层有效
  geom_point(mapping = aes(x = Sepal.Length, 
                           y = Petal.Length))

ggplot(data = iris,mapping = aes(x = Sepal.Length, y = Petal.Length))+ #此处为全局设置 对所有图层都生效
  geom_smooth()+
  geom_point()

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

ggplot(data = iris,mapping = aes(x = Species, 
                                 y = Sepal.Width,
                                 fill = Species)) + 
  geom_boxplot()+
  #geom_point(position = "jitter")
  geom_jitter() #抖动图

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() #简洁主题 theme_classic

library(ggpubr)
p = ggboxplot(iris, x = "Species", y = "Sepal.Length",
              color = "Species", shape = "Species",add = "jitter")
p
my_comparisons <- list( c("setosa", "versicolor"), 
                        c("setosa", "virginica"), 
                        c("versicolor", "virginica") ) #组间比较
p + stat_compare_means(comparisons = my_comparisons,
                       aes(label = after_stat(p.signif))) #分布叠加 aes里面的函数：显示显著性

pdf("iris_box_ggpubr.pdf")
boxplot(iris[,1]~iris[,5])
text(6.5,4, labels = 'hello')
dev.off()

p <- ggboxplot(iris, x = "Species", 
               y = "Sepal.Length",
               color = "Species", 
               shape = "Species",
               add = "jitter")
ggsave(p,filename = "iris_box_ggpubr.png")

devtools::install_github("guokai8/eoffice")
devtools::install_github("davidgohel/rvg")
BiocManager::install("davidgohel/rvg")
library(eoffice)
topptx(p,"iris_box_ggpubr.pptx")