library(ggplot2)
library(gplots)
library(RColorBrewer)
options(StringAsFactors=FALSE)
#read in the data file
data = read.table('violin_plot.txt', sep="\t", header=T)
#take a glance at the data
head(data)
dim(data)
data$EXP = log(data$ACIN1,2)
#start to draw the violin plot
p <- ggplot(data,aes(CANCER,EXP))+
geom_violin(adjust=1,trim=T)+
ggtitle("Expression of ACIN1 in different cancers")
print(p)
#changeing params
p <- ggplot(data,aes(CANCER,EXP))+
geom_violin(adjust=1,trim=T)+
geom_boxplot(width=0.3,fill="black",alpha=1,outlier.colour=NA)+
stat_summary(fun.y=mean,geom="point",fill='white',shape=21,size=3)+
theme_bw()+
theme(axis.text.x=element_text(angle=60,hjust=1,size=8),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())+
ylab('Expression level')+
xlab(NULL)+
ggtitle("Expression of ACIN1 in different cancers")
print(p)
#changing params again, mainly change the color and sort the color by mean value
#library(RColorBrewer)
color1 = brewer.pal(12,"Set3")
color2 = brewer.pal(9,"Set1")
color = c(color1,color2)
p <- ggplot(data,aes(CANCER,EXP))+
geom_violin(adjust=1,trim=T)+
geom_boxplot(width=0.3,fill=color,alpha=1,outlier.colour=NA)+
stat_summary(fun.y=mean,geom="point",fill='white',shape=21,size=2)+
theme_bw()+
theme(axis.text.x=element_text(angle=60,hjust=1,size=10),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())+
ylab('Expression level')+
xlab(NULL)+
ggtitle("Expression of ACIN1 in different cancers")
print(p)
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