r - 堆积条ggplot2上的误差线

Question

我正在努力将误差线放在堆叠条上的正确位置。正如我在之前的一篇文章中所读到的，我使用 ddply 来堆叠误差线。然后这改变了堆叠的顺序，所以我订购了这个因素。现在看起来误差条在一组条上是正确的，但在另一组上则不正确。我想要的是一个如下图所示的图表，只是带有错误栏显示的标准错误。我列出了原始数据的 dput 和 ddply 数据以及数据集。

Suz2$org <- factor(Suz2$org, levels = c('fungi','bacteria'),ordered = TRUE)

library(plyr) 
plydat <- ddply(Suz2,.(org, group, time),transform,ybegin = copy - se,yend = copy + se) 

colvec <-c("blue", "orange")

ggplot(plydat, aes(time, copy)) + 
  geom_bar(aes(fill = factor(org)), stat="identity", width = 0.7) +
  scale_fill_manual(values = colvec) +
  facet_wrap(~group,nrow = 1)+
  geom_errorbar(aes(ymax=ybegin , ymin= yend ),width=.5) +
  theme(panel.background = element_rect(fill='white', colour='white'), 
        panel.grid = element_line(color = NA),
        panel.grid.minor = element_line(color = NA),
        panel.border = element_rect(fill = NA, color = "black"),
        axis.text.x  = element_text(size=10, colour="black", face = "bold"),  
        axis.title.x = element_text(vjust=0.1, face = "bold"),
        axis.text.y = element_text(size=12, colour="black"),
        axis.title.y = element_text(vjust=0.2, size = 12, face = "bold"))

输入（plydat）

structure(list(org = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("fungi", "bacteria"
), class = c("ordered", "factor")), time = structure(c(1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L), .Label = c("0W", 
"6W"), class = "factor"), copy = c(97800000, 15500000, 40200000, 
10400000, 55100000, 14300000, 1.6e+07, 8640000, 2.98e+08, 77900000, 
2.33e+08, 2.2e+08, 3.37e+08, 88400000, 3.24e+08, 1.89e+08), group = structure(c(3L, 
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L), .Label = c("Native D0", 
"Native D707", "Notill D0", "Notill D707"), class = "factor"), 
    se = c(11100000, 2810000, 7110000, 2910000, 1.7e+07, 1500000, 
    1930000, 2980000, 43900000, 20100000, 56400000, 41200000, 
    75700000, 22500000, 57500000, 28100000), ybegin = c(86700000, 
    12690000, 33090000, 7490000, 38100000, 12800000, 14070000, 
    5660000, 254100000, 57800000, 176600000, 178800000, 261300000, 
    65900000, 266500000, 160900000), yend = c(108900000, 18310000, 
    47310000, 13310000, 72100000, 15800000, 17930000, 11620000, 
    341900000, 9.8e+07, 289400000, 261200000, 412700000, 110900000, 
    381500000, 217100000)), .Names = c("org", "time", "copy", 
"group", "se", "ybegin", "yend"), row.names = c(NA, -16L), class = "data.frame")

输入（Suz2）

structure(list(org = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("fungi", "bacteria"
), class = c("ordered", "factor")), time = structure(c(1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L), .Label = c("0W", 
"6W"), class = "factor"), copy = c(97800000, 15500000, 40200000, 
10400000, 55100000, 14300000, 1.6e+07, 8640000, 2.98e+08, 77900000, 
2.33e+08, 2.2e+08, 3.37e+08, 88400000, 3.24e+08, 1.89e+08), group = structure(c(3L, 
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L), .Label = c("Native D0", 
"Native D707", "Notill D0", "Notill D707"), class = "factor"), 
    se = c(11100000, 2810000, 7110000, 2910000, 1.7e+07, 1500000, 
    1930000, 2980000, 43900000, 20100000, 56400000, 41200000, 
    75700000, 22500000, 57500000, 28100000)), .Names = c("org", 
"time", "copy", "group", "se"), row.names = c(NA, -16L), class = "data.frame")

苏兹2

  org time     copy       group       se
1     fungi   0W 9.78e+07   Notill D0 11100000
2     fungi   0W 1.55e+07 Notill D707  2810000
3     fungi   0W 4.02e+07   Native D0  7110000
4     fungi   0W 1.04e+07 Native D707  2910000
5     fungi   6W 5.51e+07   Notill D0 17000000
6     fungi   6W 1.43e+07 Notill D707  1500000
7     fungi   6W 1.60e+07   Native D0  1930000
8     fungi   6W 8.64e+06 Native D707  2980000
9  bacteria   0W 2.98e+08   Notill D0 43900000
10 bacteria   0W 7.79e+07 Notill D707 20100000
11 bacteria   0W 2.33e+08   Native D0 56400000
12 bacteria   0W 2.20e+08 Native D707 41200000
13 bacteria   6W 3.37e+08   Notill D0 75700000
14 bacteria   6W 8.84e+07 Notill D707 22500000
15 bacteria   6W 3.24e+08   Native D0 57500000
16 bacteria   6W 1.89e+08 Native D707 28100000

Answer 1

和的值ybegin，yend即误差线的范围，对于数据来说太低了bacteria。由于条形图位于条形图的bacteria顶部，因此必须将条形图 ( )fungi的高度添加到数据的误差线值中。fungiplydat$copy[plydat$org == "fungi"]bacteria

plydat[plydat$org == "bacteria", ] 
   <- transform(plydat[plydat$org == "bacteria", ],
                ybegin = ybegin + plydat[plydat$org == "fungi", "copy"], 
                yend = yend + plydat[plydat$org == "fungi", "copy"])

Answer 2

就个人而言，我不是很喜欢堆叠条形图，尤其是当堆叠条的数量很大时（您不是这种情况）。主要问题是除了最低堆栈之外的所有堆栈都不共享相同的基线。在您的情况下，很难比较橙色bacteria类，因为它们不共享相同的基数（y 值，copy）。

我建议使用一个称为点图的图：

library(ggplot2)
theme_set(theme_bw())
ggplot(plydat, aes(time, copy, color = org)) + 
   geom_point() + facet_wrap(~group, ncol = 1) + 
   geom_errorbar(aes(ymax=ybegin , ymin= yend), width = 0) + coord_flip()

请注意，copy此处的值不是累加的，因为它在堆叠条形图中。因为它们共享相同的基copy值 (0)，您可以轻松地比较 的不同值bacteria。此外，我交换了 x 和 y 轴以方便比较 的值copy（只需删除coord_flip以查看在比较中的效果如何copy）。

唯一真正的缺点是没有简单的方法来判断 和 的fungi总和bacteria。根据图表要显示的内容（图表的故事），这可能是也可能不是问题。您可以向 中添加一个单独的附加类别org，即both两个类别的总和，以解决此问题。当然，解释这个总和类别中的错误并非易事。

Answer 3

从上述答案的组合中，我想我会选择这样的东西。

plydat <- ddply(Suz2,.(org),transform,ybegin = copy - se,yend = copy + se)   

colvec <-c("blue", "orange")

ggplot(plydat, aes(time, copy, color = factor(org))) + 
   geom_point(size = 3.5) + facet_wrap(~group, ncol = 4) + 
   scale_color_manual(values = colvec) +
   geom_errorbar(aes(ymax=ybegin , ymin= yend), width = 0.08, 
        color = "black", size = 0.1) +
   theme(panel.background = element_rect(fill='white', colour='white'), 
        panel.grid = element_line(color = NA),
        panel.grid.minor = element_line(color = NA),
        panel.border = element_rect(fill = NA, color = "black"),
        strip.background = element_blank(),
        axis.text.x  = element_text(size=10, colour="black", face = "bold"),  
        axis.title.x = element_text(vjust=0.1, face = "bold"),
        axis.text.y = element_text(size=12, colour="black"),
        axis.title.y = element_text(vjust=0.2, size = 12, face = "bold"))