使用填充、颜色和 alpha 使用 geom_bar 躲避 geom_errorbar

Question

我正在尝试制作一个带有误差线 (se) 的 facet_wrap bar_graph，它清楚地显示了三个不同的分类变量（治疗、地平线、酶）和一个响应变量 (AbundChangetoAvgCtl)。下面是一些虚拟数据的代码，后面是我到目前为止的 ggplot 代码。我制作的图表可以在这个链接中看到： bargraph figures

Enzyme <- c("Arabinosides","Arabinosides","Arabinosides","Arabinosides","Arabinosides","Arabinosides","Cellulose","Cellulose","Cellulose","Cellulose","Cellulose","Cellulose","Chitin","Chitin","Chitin","Chitin","Chitin","Chitin","Lignin","Lignin","Lignin","Lignin","Lignin","Lignin")
Treatment <- c("Deep","Deep","Int","Int","Low","Low","Deep","Deep","Int","Int","Low","Low","Deep","Deep","Int","Int","Low","Low","Deep","Deep","Int","Int","Low","Low")
Horizon <- c("Org","Min","Org","Min","Org","Min","Org","Min","Org","Min","Org","Min","Org","Min","Org","Min","Org","Min","Org","Min","Org","Min","Org","Min")
AbundChangetoAvgCtl <- rnorm(24,mean=0,sd=1)
se <- rnorm(24, mean=0.5, sd=0.25)
notrans_noctl_enz_toCtl_summary <- data.frame(Enzyme,Treatment,Horizon,AbundChangetoAvgCtl,se)
ggplot(notrans_noctl_enz_toCtl_summary, aes(x=Horizon, y=AbundChangetoAvgCtl, fill=Horizon, alpha=Treatment)) +
  geom_bar(position=position_dodge(), colour="black", stat="identity", aes(fill=Horizon)) +
  geom_errorbar(aes(ymin=AbundChangetoAvgCtl-se, ymax=AbundChangetoAvgCtl+se),
            width=.2,
            position=position_dodge(.9)) + 
  scale_fill_brewer(palette = "Set1") + theme_bw() +
  geom_hline(yintercept=0) +
  labs(y = "Rel Gene Abundance Change / Control", x="") +
  theme(axis.ticks = element_blank(), 
        axis.text.x = element_blank(),
        strip.text.x = element_text(size=20),
        plot.title = element_text(size=22, vjust=2, face="bold"),
        axis.title.y = element_text(size=18),
        legend.key.size = unit(.75, "in"),
        legend.text = element_text(size = 15),
        legend.title = element_text(size = 18)) +
  facet_wrap(~Enzyme, scales="free")

（图一）

所以这接近我想要的，但是由于某种原因，ggplot 中的“alpha=Treatment”调用导致我的错误栏消失（我不想要）以及 bar_fill（我想要） .我已经尝试将“alpha=Treatment”移动到 geom_bar 调用，以及将“alpha=1”添加到 geom_bar，但是当我这样做时，误差条都会移动到一个位置并重叠（图 2）。

我最初想在 facet_wrap 中聚集条形图，但在这个网站上找到了 alpha 选项，这似乎也完成了我正在寻找的东西。任何帮助，将不胜感激。如果有更好的方式来代表所有这些，那么这些想法也是受欢迎的。
还有，如果有什么方法可以把我的传说浓缩和澄清，那将是额外的奖励！ 提前感谢您的帮助！

迈克

Answer 1

您需要将Treatment 分配给ggplot() 命令中的group 选项，然后将alpha=Treatment 选项移动到geom_bar() 命令。那么alpha 的值geom_errorbar 将不受全局选项的影响，将变为黑色。像这样：

ggplot(notrans_noctl_enz_toCtl_summary, aes(x=Horizon, y=AbundChangetoAvgCtl, fill=Horizon, group = Treatment)) +
  geom_bar(position=position_dodge(), colour="black", stat="identity", aes(fill=Horizon, alpha = Treatment)) 

另外，我会检查设置alpha=Treatment 是否对应于更透明，相当于低处理，而不是高处理透明度。至少这是我的直觉理解，没有任何研究设计或数据背景。

有关格式化图例的信息，请参阅here。