堆积条ggplot2上的误差线

Question

我正在努力将误差棒放在堆积条上的正确位置.正如我在之前的帖子中读到的那样,我使用ddply来堆叠错误栏.然后,这改变了堆叠的顺序,所以我订购了因子.现在看来,错误条在一组条形图上是正确的而在另一组条形图上是正确的.我想要的是一个如下图所示的图表,只是显示带有误差条的标准误差.我列出了原始数据和ddply数据以及数据集的输入.

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"))

dput(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")

dput(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")

Suz2

  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

两者的值ybegin和yend错误栏的范围对于bacteria数据来说太低了.由于条形图位于条形图的bacteria顶部,因此fungi条形图fungi(plydat$copy[plydat$org == "fungi"])的高度必须添加到bacteria数据的误差条值中.

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,我并不是真的喜欢堆积的条形图,特别是当堆积的条形数量很大时(对你来说情况并非如此).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).

我建议使用一个名为dotplot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此处的值不是叠加条形图中的附加值.因为它们共享相同的基copy值(0),所以您可以轻松地比较不同的值bacteria.另外,我交换了x轴和y轴,以便于比较它的值copy(只需删除它coord_flip以查看比较中有多糟糕copy).

唯一真正的缺点是,有判断的总和没有简单的方法fungi和bacteria.根据图表的显示内容(图表的故事),这可能是也可能不是问题.您可以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.