title: "ggplot2绘制火山图"
output: html_document

knitr::opts_chunk$set(echo = TRUE)

第一步：初步了解ggplot2

创建画布

library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) 

在画布上添加图层（几何图像，散点图

library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point()

将direction映射给点的颜色

library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction))

换个主题//

library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction)) +
  theme_bw()

（标度控制映射的方式[颜色]

library(ggplot2)
library(ggsci)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction)) +
  scale_color_npg()+
  theme_bw()

  

ggplot2涉及到的思想：

1.图层2.映射3.标度4.主题

步骤二：深入理解

修改点的颜色

my_palette <- c('#66CC33','#9999CC','#FF6699')
library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction))+
  scale_color_manual(values = my_palette)+
  theme_bw()

修改点的大小

my_palette <- c('#66CC33','#9999CC','#FF6699')
library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction, size = abs(log2FoldChange)))+
  scale_size(range = c(0.1,3))+
  scale_color_manual(values = my_palette)+
  theme_bw()

修改点的透明度

my_palette <- c('#66CC33','#9999CC','#FF6699')
library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction, size = abs(log2FoldChange),alpha = abs(log2FoldChange)))+
  scale_size(range = c(0.1,3))+
  scale_color_manual(values = my_palette)+
  theme_bw()

#修改点的透明度
```{r}
my_palette <- c('#66CC33','#9999CC','#FF6699')
library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction, size = abs(log2FoldChange),alpha = abs(log2FoldChange)))+
  scale_size(range = c(0.1,3))+
  scale_color_manual(values = my_palette)+
  theme_bw()

添加阈值线条

my_palette <- c('#66CC33','#9999CC','#FF6699')
library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction, size = abs(log2FoldChange),alpha = abs(log2FoldChange)))+
  geom_hline(yintercept = -log10(0.05),linetype = 'dashed')+
  geom_vline(xintercept = c(-1,1),linetype = 'dashed')+
  scale_size(range = c(0.1,3))+
  scale_color_manual(values = my_palette)+
  theme_bw()

标题居中

library(ggrepel)
my_palette <- c('#66CC33','#9999CC','#FF6699')
library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction, size = abs(log2FoldChange),alpha = abs(log2FoldChange)))+
  geom_hline(yintercept = -log10(0.05),linetype = 'dashed')+
  geom_vline(xintercept = c(-1,1),linetype = 'dashed')+
  geom_label_repel(data = top_de,aes(label = Gene_Symbol))+
  scale_size(range = c(0.1,3))+
  scale_color_manual(values = my_palette)+
  labs(x = 'log2 fold change',
       y = '-log10 (pvalue)',
       title = 'volcano plot',
       size = 'log2 fold change')+
theme_bw()+
theme(plot.title = element_text(size = 20 ,hjust = 0.5))

删掉一个图例&修改图例位置

library(ggrepel)
my_palette <- c('#66CC33','#9999CC','#FF6699')
library(ggplot2)
ggplot(data = de_result , aes(x = log2FoldChange , y = -log10(padj))) +
  geom_point(aes(color = direction, size = abs(log2FoldChange),alpha = abs(log2FoldChange)))+
  geom_hline(yintercept = -log10(0.05),linetype = 'dashed')+
  geom_vline(xintercept = c(-1,1),linetype = 'dashed')+
  geom_label_repel(data = top_de,aes(label = Gene_Symbol))+
  scale_size(range = c(0.1,3))+
  scale_color_manual(values = my_palette)+
  labs(x = 'log2 fold change',
       y = '-log10 (pvalue)',
       title = 'volcano plot',
       size = 'log2 fold change',
       color = ' ')+
#color = ' ' 将图例中direction去掉
theme_bw()+
theme(plot.title = element_text(size = 20 ,hjust = 0.5),
      legend.background = element_blank(),
      legend.position = c(0.9,0.6))+
  guides(size = FALSE)