画单图
expr$Sam <- factor(expr$Sam,levels = c("Young","Aged"))
p <- ggviolin(subset(expr,Id3 >0), x = "Sam", # 分组列
y = "Id3", # 基因列
fill = "Sam", #按分组填充颜色
alpha = 1,#透明图 0-1
width = 0.5, #宽度
legend = "top",legend.title = "Group",#legend及位置
font.legend = c(12, "bold", "black"),
# ylim=c(0, 4), #y轴长度
ylab="Expression levels", xlab=FALSE, #xy轴标签，去掉X轴标签
font.y = 16,#xy轴标题大小
x.text.angle = 45, y.text.angle = 90,#xy轴标题角度
font.tickslab = c(15,"plain","black"), #xy轴刻度大小/样式/颜色
add = "boxplot", #添加图 "dotplot", "jitter", "boxplot", "point"
add.params = list(fill = "white", #填充颜色 白色
width = 0.1,#宽度
linetype = 1),#线型
palette ="jco" #调色板调色如c("blue", "red")
# 也可以直接按杂志来改，如 "npg", "aaas", "lancet",
# "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
)
# my_comparisons <- list(c("0", "1"), c("0", "2"), c("0", "3"), c("0" ,"4"))##多分组设定比较
# my_comparisons <- list(c("0", "1"))##多分组设定比较
p <- p + stat_compare_means(method = "t.test",
label = "p.signif",##星号设置
aes(label = "p.format"), #显示方式
label.x.npc ="middle",
# label.y = 3.2,#位置
size = 5,
# comparisons = my_comparisons
)
p
ggsave("Id3 _Sam.pdf",width=2.3,height=4)
image.png
批量画图
#批量画图
plist<-list()
for (i in 1:length(genes)){
expr_tmp<-expr[,c(genes[i],"Sam")]
pb1 <- ggviolin(subset(expr_tmp,genes[i]>0), x = "Sam", # 分组列
y = genes[i], # 基因列
fill = "Sam", #按分组填充颜色
alpha = 1,#透明图 0-1
width = 0.5, #宽度
legend = "top",legend.title = genes[i],#legend及位置
font.legend = c(12, "bold", "black"),
# ylim=c(0, 4), #y轴长度
ylab="Expression levels", xlab=FALSE, #xy轴标签，去掉X轴标签
font.y = 16,#xy轴标题大小
x.text.angle = 45, y.text.angle = 90,#xy轴标题角度
font.tickslab = c(15,"plain","black"), #xy轴刻度大小/样式/颜色
add = "boxplot", #添加图 "dotplot", "jitter", "boxplot", "point"
add.params = list(fill = "white", #填充颜色 白色
width = 0.1,#宽度
linetype = 1),#线型
palette ="jco" #调色板调色如c("blue", "red")
# 也可以直接按杂志来改，如 "npg", "aaas", "lancet",
# "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
)
# +
stat_compare_means(method="t.test",hide.ns = F,comparisons =my_comparisons,label="p.signif")
plist[[i]]<-pb1
}
# cowplot
library(cowplot)
p <- plot_grid(plotlist = plist, ncol = 6)
ggsave("boxplot1208.pdf",width = 14,height = 4)
image.png
