散点图

library(ggplot2)
df1 <- read.csv("scatter_plot_example.csv",header=T)
head(df1)

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ggplot(data=df1,aes(x=var1,y=var2)) + geom_point()

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ggplot(data=df1,aes(x=var1,y=var2)) +
  geom_point(color="red",size=10,shape=18,alpha=0.5)

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ggplot(data=df1,aes(x=var1,y=var2,color=var3,shape=var3)) +
  geom_point(size=5)

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ggplot(data=df1,aes(x=var1,y=var2,color=var3,shape=var3)) +
  geom_point(size=5) +
  scale_color_manual(values=c("steelblue","yellowgreen","violetred1"))

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ggplot(data=df1,aes(x=var1,y=var2,color=var3,shape=var3)) +
  geom_point(size=5) +
  scale_color_manual(values=c("steelblue","yellowgreen","violetred1")) +
  scale_shape_manual(values=c(9,10,11))

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气泡图

df2 <- read.csv("bubble_plot_example.csv",header=T)
head(df2)

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ggplot(data=df2,aes(x=var1,y=var2,color=var3,size=var4)) +
  geom_point(alpha=0.8) +
  scale_size_continuous(range=c(1,50)) +
  theme_bw() +
  theme(legend.position="none") +
  ylim(0,0.4) +
  scale_color_manual(values=c("steelblue","yellowgreen","violetred1"))

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折线图

df3 <- read.csv("line_example.csv",header=T)
head(df3)

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ggplot(data=df3,aes(x=time_point,y=value)) +
  geom_line() +
  geom_point() +
  geom_errorbar(aes(ymin=value-sd,ymax=value+sd),width=0.15) +
  theme_bw()

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柱形图

df4 <- read.csv("bar_plot_example.csv",header=T)
head(df4)

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ggplot(data=df4,aes(x=var1,y=var2)) + geom_col()

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ggplot(data=df4,aes(x=var1,y=var2)) +
  geom_col(color="red",fill="lightblue")

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ggplot(data=df4,aes(x=var1,y=var2)) +
  geom_col(aes(fill=var1)) +
  theme_bw() +
  scale_fill_manual(values=c("#008fd5","#ff2700","#77ab43","#ffd700")) +
  scale_y_continuous(expand=c(0,0),limits=c(0,8))

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df5 <- read.csv("bar_plot_example_1.csv",header=T)
head(df5)

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ggplot(data=df5,aes(x=var3,y=var2,fill=var1)) +
  geom_bar(stat="identity") +
  theme_bw() +
  scale_fill_manual(values=c("steelblue","yellowgreen","violetred1")) +
  scale_y_continuous(expand=c(0,0),limits=c(0,20))

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ggplot(data=df5,aes(x=var3,y=var2,fill=var1)) +
  geom_bar(stat="identity",position="dodge") +
  scale_fill_manual(values=c("steelblue","yellowgreen","violetred1")) +
  scale_y_continuous(expand=c(0,0),limits=c(0,10)) +
  theme_bw()

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箱线图

df6 <- read.csv("ToothGrowth.csv",header=T)
head(df6)
table(df6$dose)

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df6$dose <- factor(df6$dose,levels=c("0.5","1","2"))

ggplot(data=df6,aes(x=dose,y=len,fill=dose)) +
  geom_boxplot() +
  scale_fill_manual(values=c("steelblue","yellowgreen","violetred1")) +
  theme_bw() +
  stat_boxplot(geom="errorbar",width=0.2)

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小提琴图

ggplot(data=df6,aes(x=dose,y=len,fill=dose)) +
  geom_violin() +
  theme_bw() +
  scale_fill_manual(values=c("steelblue","yellowgreen","violetred1"))

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ggplot(data=df6,aes(x=dose,y=len,fill=dose)) +
  geom_violin() +
  geom_boxplot(width=0.3) +
  scale_fill_manual(values=c("steelblue","yellowgreen","violetred1")) +
  theme_bw() +
  stat_boxplot(geom="errorbar",width=0.2)

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热图

df7 <- read.csv("pheatmap_example_data.csv",header=T)
head(df7)

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library(reshape2)
df7.1 <- melt(df7,id.vars='gene_name')
head(df7.1)

ggplot(data=df7.1,aes(x=variable,y=gene_name,fill=value)) +
  geom_tile(color="black") +
  theme(axis.text.x=element_text(angle=90,hjust=0.5,vjust=0.5),axis.ticks=element_blank()) +
  scale_fill_gradient(low="steelblue",high="violetred1") +
  labs(x=NULL,y=NULL) +
  geom_text(aes(label=round(value,1)))

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