R中的ggplot2中用於2x2x2設計的堆疊條形圖

Question

我有一個看起來像這樣的數據集：

conifer.abundance <- c(6,7,8,2,3,4,5,1,7,8,9,8,7,6,5,1)
lily.abundance <- c(5,5,5,5,4,4,4,4,6,7,8,2,3,4,5,1)
type <- c("Control","Control","Control","Control","Control","Control","Control","Control","Treatment","Treatment","Treatment","Treatment","Treatment","Treatment","Treatment","Treatment")
class <- c("City","Rural","City","Rural","City","Rural","City","Rural","City","Rural","City","Rural","City","Rural","City","Rural")
climate <- c("wet","wet","dry","dry","wet","wet","dry","dry","wet","wet","dry","dry","wet","wet","dry","dry")
all.abundance <- conifer.abundance + lily.abundance
dat88 <- data.frame(climate,type,class,conifer.abundance, lily.abundance,all.abundance)

這是2x2x2的設計。 我想繪制條形圖，以便將all.abundance的均值表示為mean conifer.abundance和mean lily.abundance（堆疊）的總和，並且它具有自己的傳說。 我嘗試遵循此代碼，但是似乎使用fill來堆積條形圖，但是在這里我需要將其用於其他目的。 假設我還有幾個數據點，我還需要繪制一個自舉的置信區間（如下所示）。 有什么建議么？ 這是我目前用於繪制上面圖形的代碼。

  pd <- position_dodge(0.82) 
  ggplot(dat88, aes(x=class, y=all.abundance, fill = climate)) + 
  theme_bw() + 
  stat_summary(geom="bar", fun.y=mean, position = "dodge") + 
  stat_summary(geom="errorbar", fun.data=mean_cl_boot,position = pd) + 
  ylab("Total Abundance") + 
  facet_grid(~type)

請注意，我略微更改了數據集以代表更符合生物學的情況。

Answer 1

如果要堆疊女性和男性的身高值，則需要將其融化/收集到單個變量中。

以下兩種用於操縱數據幀的方法是等效的。 取決於您更熟悉哪些軟件包：

# data.table package
dat2 <- data.table::melt(dat, measure.vars = c("male.height", "female.height"),
                         variable.name = "Gender", value.name = "height")

# tidyr package
dat3 <- tidyr::gather(dat, key = Gender, value = height, 
                      male.height, female.height, factor_key = TRUE)

> all.equal(dat2, dat3)
[1] TRUE

由於這是2 x 2 x 2的設計，因此我向facet_grid添加了一個尺寸，以顯示類型和種類。 如果不需要，只需恢復為facet_grid(~type) ：

ggplot(dat2,
       aes(x = class, y = height, fill = Gender)) +
  geom_col() +
  ylab("Total Height") +
  facet_grid(species~type) +
  scale_fill_discrete(breaks = c("female.height", "male.height"),
                      labels = c("female", "male"))