abline和stat_smooth的ggplot2圖例

Question

我有ggplot傳說的一些問題，這是我的第一個代碼只有corrGenes的圖例，這很好。

gene1=c(1.041,0.699,0.602,0.602,2.585,0.602,1.000,0.602,1.230,1.176,0.699,0.477,1.322)
    BIME = c(0.477,0.477,0.301,0.477,2.398,0.301,0.602,0.301,0.602,0.699,0.602,0.477,1.176)
    corrGenes=c(0.922,0.982,0.934,0.917,0.993,0.697,0.000,0.440,0.859,0.788,0.912,0.687,0.894)

DF=data.frame(gene1,BIME,corrGenes)

plot= ggplot(data=DF,aes(x=gene1,y=BIME))+
  geom_point(aes(colour=corrGenes),size=5)+
  ylab("BIME normalized counts (log10(RPKM))")+
  xlab("gene1 normalized counts (log10(RPKM))")

當我添加abline和smooth時，我得到了正確的情節：

plot= ggplot(data=DF,aes(x=gene1,y=BIME))+
  geom_point(aes(colour=corrGenes),size=5)+
  geom_abline(intercept=0, slope=1)+
  stat_smooth(method = "lm",se=FALSE)+
  ylab("BIME normalized counts (log10(RPKM))")+
  xlab("gene1 normalized counts (log10(RPKM))")

但沒有辦法得到他們的傳說，我嘗試了許多其他組合：

plot= ggplot(data=DF,aes(x=gene1,y=BIME))+
  geom_point(aes(colour=corrGenes),size=5)+
  geom_abline(aes(colour="best"),intercept=0, slope=1)+
  stat_smooth(aes(colour="data"),method = "lm",se=FALSE)+
  scale_colour_manual(name="Fit", values=c("data"="blue", "best"="black"))+
  ylab("BIME normalized counts (log10(RPKM))")+
  xlab("gene1 normalized counts (log10(RPKM))")

如果有人有想法解決這個微小但非常惱人的問題，那將非常有幫助！

Answer 1

最后，我找到了使用技巧的方式。 首先，我計算了線性回歸並將結果轉換為數據框，我添加了最合適的數據（Intercept = 0和slope = 1），然后我添加了一列數據類型（數據或最佳）。

modele = lm(BIME ~ gene1, data=DF)
coefs = data.frame(intercept=coef(modele)[1],slope=coef(modele)[2])
coefs= rbind(coefs,list(0,1))
regression=as.factor(c('data','best'))
coefs=cbind(coefs,regression)

然后我用一個獨特的geom_abline命令繪制它並將DF從ggplot（）移動到geom_point（）並使用linetype參數來區分這兩行：

plot = ggplot()+
  geom_point(data=pointSameStrandDF,aes(x=gene1,y=BIME,colour=corrGenes),size=5)+
  geom_abline(data=coefs, aes(intercept=intercept,slope=slope,linetype=regression), show_guide=TRUE)+
  ylab("BIME normalized counts (log10(RPKM))")+
  xlab("gene1 normalized counts (log10(RPKM))")

也許有一種方法可以使用這兩行的顏色，但我不知道如何？

謝謝你的幫助！

Answer 2

show_guide=TRUE參數應顯示geom_abline和stat_smooth 。 嘗試運行以下代碼。

plot= ggplot(data=DF,aes(x=gene1,y=BIME))+
geom_point(aes(colour=corrGenes),size=5)+
geom_abline(aes(colour="best"),intercept=0, slope=1, show_guide=TRUE)+
stat_smooth(aes(colour="data"),method = "lm",se=FALSE, show_guide=TRUE)+
scale_colour_manual(name="Fit", values=c("data"="blue", "best"="black"))+
ylab("BIME normalized counts (log10(RPKM))")+
xlab("gene1 normalized counts (log10(RPKM))")

Answer 3

不確定這是否是最佳解決方案，但我能夠告訴ggplot有兩個刻度，一個用於顏色（你的點），另一個用於填充顏色。 你可能會問哪種顏色？ 我在兩條線的aes添加的那個：

plot = ggplot(data=DF,aes(x=gene1,y=BIME)) + 
  geom_point(size=5, aes(colour=corrGenes)) +
  geom_abline(aes(fill="black"),intercept=0, slope=1) + 
  stat_smooth(aes(fill="blue"), method = "lm",se=FALSE) +
  scale_fill_manual(name='My Lines', values=c("black", "blue"))+
  ylab("BIME normalized counts (log10(RPKM))")+
  xlab("gene1 normalized counts (log10(RPKM))")