ggplot2条形图中条形的顺序和颜色

Question

使用创建的堆积条形图我有一个非常烦人的问题ggplot2.之前有几个类似的问题,但在完成示例代码后,我无法弄清楚我做错了什么.

我想制作图表,以便按照以下顺序堆叠条形图Biogeographic.affinity:(从上到下= Bassian,Widespread,Torresian和Eyrean).条形的颜色应为:( Bassian = drakgrey,Widespread = lightgrey,Torresian = white,Eyrean = black).

这就是数据集的样子:

  biogeo
       Site Biogeographic.affinity Rank Number.of.species Total.Species    Percent
    1     A                Bassian    1                 1           121  0.8264463
    2     A                 Eyrean    4                39           121 32.2314050
    3     A              Torresian    3                62           121 51.2396694
    4     A             Widespread    2                19           121 15.7024793
    5    DD                Bassian    1                 1           128  0.7812500
    6    DD                 Eyrean    4                46           128 35.9375000
    7    DD              Torresian    3                63           128 49.2187500
    8    DD             Widespread    2                18           128 14.0625000
    9   E_W                Bassian    1                 1           136  0.7352941
    10  E_W                 Eyrean    4                54           136 39.7058824
    11  E_W              Torresian    3                65           136 47.7941176
    12  E_W             Widespread    2                16           136 11.7647059
    13   KS                Bassian    1                 2           145  1.3793103
    14   KS                 Eyrean    4                63           145 43.4482759
    15   KS              Torresian    3                62           145 42.7586207
    16   KS             Widespread    2                18           145 12.4137931
    17 Z_Ka                Bassian    1                 1           110  0.9090909
    18 Z_Ka                 Eyrean    4                64           110 58.1818182
    19 Z_Ka              Torresian    3                31           110 28.1818182
    20 Z_Ka             Widespread    2                14           110 12.7272727

这是我到目前为止编写的代码(包括我纠正问题的一些失败尝试).

 ggplot(data=biogeo, aes(x=Site, y=Percent, fill=Biogeographic.affinity)) + geom_bar(stat="identity", colour="black")+ 
  scale_fill_grey() + ylab("Percent") + xlab("Location") +       
  theme_bw()+ theme(panel.grid.minor = element_blank()) 

这给出了基本图形,但颜色和顺序仍然是错误的.为了纠正我尝试的顺序,但这并没有改变任何东西(FRUSTRATED)!:

newone <- transform(biogeo, Biogeographic.affinity  = factor(Biogeographic.affinity ), Rank = factor(Rank, levels = 1:4))

至于颜色变化,我已经尝试过,似乎工作,但它看起来像订单仍然是错误的!

cols<- c("Bassian"="darkgrey","Widespread"="lightgrey", "Torresian"="white", "Eyrean"="black") #designates the colors of the bars 
ggplot(data=newone, aes(x=Site, y=Percent, fill=Biogeographic.affinity)) + geom_bar(stat="identity", colour="black")+ 
  scale_fill_manual(values = cols) + ylab("Percent") + xlab("Location") +       
  theme_bw()+ theme(panel.grid.minor = element_blank()) 

请帮忙.

Answer 1

在ggplot2中堆叠的条形图中绘制条形图(从下到上)的顺序基于定义组的因子的顺序.因此必须重新排序Biogeographic.affinity因子.通常我们使用reorder(如果我们想按照连续的水平对因子进行排序),但在这里我将创建一个类似于您尝试的新的有序因子.

 biogeo <- transform(biogeo, 
                Biog.aff.ord  = factor(
                     Biogeographic.affinity ,
                     levels=c( 'Bassian','Widespread','Torresian', 'Eyrean'),
                     ordered =TRUE))

现在,如果您使用Biog.aff.ord填充条形图而不是原始因子,并通过将aes_group_order定义为Biog.aff.ord顺序来覆盖默认分组顺序,则会得到预期结果:

cols <- c(Bassian="darkgrey",Widespread="lightgrey", 
            Torresian="white", Eyrean="black") 
ggplot(data=biogeo, aes(x=Site, y=Percent,
       order=Biog.aff.ord)) +   ##!! aes_group_order
  geom_bar(stat="identity", colour="black",
        aes(fill=Biog.aff.ord)) +
  scale_fill_manual(values = cols)