嘗試復現(xiàn)文章的過程中亿汞，運用生信技能樹jimmy大大的搜索神技羔沙，順利整理出了一幅看著還不錯的火山圖，用的包是ggplot2伟骨，分享一下饮潦，共同學習進步！
首先用dplyr包挑選作圖列携狭， mutate(v= -log10(adj.P.Val)增加一列（y軸）继蜡，以case_when（）將基因根據(jù)abs（logFC）>=2&adj.P.Val(FDR) < 0.01分為上調(diào)下調(diào)及穩(wěn)定基因。
通過一系列函數(shù)對橫坐標range進行了限定暑中，本例子中所得x軸（abs（logFC））最大值為6壹瘟，所以橫軸坐標修改為了（-6，6）鳄逾。
其他自主修改的參數(shù)有顏色，透明度灵莲，以及圖形大小雕凹。emmmm，個人感覺漸變不太好看（可能不習慣太淺的顏色）。
if(T){
library(dplyr)
library(tidyverse)
library(ggplot2)
DEG_valvone <- nrDEG
colnames(DEG_valvone)
DEG_valvone <- DEG_valvone %>%
select(logFC,AveExpr, adj.P.Val) %>%
mutate(v= -log10(adj.P.Val),
gene_type = case_when(logFC >= 2 & adj.P.Val < 0.01 ~ "up",
logFC <= -2 & adj.P.Val < 0.01 ~ "down",
TRUE ~ "stable"))
##查看x坐標軸設(shè)定范圍
DEG_valvone %>%
pull(logFC) %>%
min() %>%
floor() #查看x軸最小邊界 -5
DEG_valvone %>%
pull(logFC) %>%
max() %>%
ceiling() #最大邊界6
###設(shè)定上調(diào)下調(diào)穩(wěn)定點顏色大小透明度
cols <- c("up" = "#ffad73", "down" = "#26b3ff", "stable" = "grey")
sizes <- c("up" = 2, "down" = 2, "stable" = 1)
alphas <- c("up" = 1, "down" = 1, "stable" = 0.5)
}
final_plot <- DEG_valvone %>%
ggplot(aes(x = logFC,
y = v,
fill = gene_type,
size = gene_type,
alpha = gene_type)) +
geom_point(shape = 21, # Specify shape and colour as fixed local parameters
colour = "black") +
geom_hline(yintercept = -log10(0.01),
linetype = "dashed") +
geom_vline(xintercept = c(-2, 2),
linetype = "dashed") +
scale_fill_manual(values = cols) + # Modify point colour
scale_size_manual(values = sizes) + # Modify point size
scale_alpha_manual(values = alphas) + # Modify point transparency
scale_x_continuous(breaks = c(seq(-6, 6, 1)),
limits = c(-6, 6))+
labs(title = "Gene expression changes in Vemurafenib versus control samples",
x = "log2(fold change)",
y = "-log10(adjusted P-value)",
colour = "Expression \nchange") +
theme_bw() + # Select theme with a white background
theme(panel.border = element_rect(colour = "black", fill = NA, size= 0.5),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank())
final_plot
ggsave("valcone_plot.png",plot = final_plot,width = 200,height = 150,units ="mm" )
valcone_plot.png
