着色ggplot

Question

我有以下data.frame：

mean std.dev haplotype tissue genotype replicate 
-4.60517018598809 0 hap1 Brain - Amygdala het 1 
-4.60517018598809 0 hap1 Brain - Amygdala het 2 
-4.60517018598809 0 hap1 Brain - Amygdala het 3 
-4.60517018598809 0 hap1 Brain - Amygdala hom 4 
-4.60517018598809 0 hap1 Brain - Amygdala hom 5 
-2.4087395856822 2.0768401930033 hap1 Brain - Caudate (basal ganglia) het 6 
-2.33089555210139 1.22454341404608 hap1 Brain - Caudate (basal ganglia) het 7 
-1.99693736361828 0.942996853632486 hap1 Brain - Caudate (basal ganglia) het 8 
-2.86324165970641 1.11947980609972 hap1 Brain - Caudate (basal ganglia) het 9 
-4.60517018598809 0 hap1 Brain - Caudate (basal ganglia) het 10 
-4.60517018598809 0 hap1 Brain - Caudate (basal ganglia) het 11 
-4.60517018598809 0 hap1 Brain - Caudate (basal ganglia) het 12 
-4.60517018598809 0 hap1 Brain - Caudate (basal ganglia) het 13 
-4.60517018598809 0 hap1 Brain - Caudate (basal ganglia) het 14 
-4.60517018598809 0 hap1 Brain - Caudate (basal ganglia) het 15 
-1.90227490544572 1.3118533678251 hap1 Brain - Caudate (basal ganglia) het 16 
-4.60517018598809 0 hap1 Brain - Caudate (basal ganglia) hom 17 
-2.28388358957011 1.66055627514132 hap1 Brain - Caudate (basal ganglia) hom 18 
-3.18075788363206 1.31500305472203 hap1 Brain - Caudate (basal ganglia) hom 19 
-4.60517018598809 0 hap1 Brain - Caudate (basal ganglia) hom 20 
-2.99628156173586 1.45715378560505 hap1 Brain - Frontal Cortex (BA9) het 21 
-4.60517018598809 0 hap1 Brain - Frontal Cortex (BA9) hom 22 
-4.60517018598809 0 hap1 Brain - Frontal Cortex (BA9) hom 23 
-4.60517018598809 0 hap1 Brain - Frontal Cortex (BA9) hom 24 
-4.60517018598809 0 hap1 Brain - Frontal Cortex (BA9) hom 25 
-4.60517018598809 0 hap1 Brain - Frontal Cortex (BA9) hom 26 
-4.60517018598809 0 hap1 Brain - Hippocampus het 27 
-3.23659805518369 1.30083340138879 hap1 Brain - Hippocampus het 28 
-2.53609036554034 1.4874106990496 hap1 Brain - Hippocampus hom 29 
-3.09405707251877 1.2828530102749 hap1 Brain - Hippocampus hom 30 
-2.96062268602418 1.43770353838178 hap1 Brain - Hippocampus hom 31 
-2.77211009494142 1.20159646882509 hap1 Brain - Hippocampus hom 32 
-0.363072614934047 0.458485378139217 hap1 Brain - Hippocampus hom 33 
-2.32474357410041 1.08129672683285 hap1 Brain - Hippocampus hom 34 
-3.22834640282763 1.32315679407156 hap1 Brain - Hippocampus hom 35 
-3.14051445752854 1.47382291072761 hap1 Brain - Hypothalamus hom 36 
-2.75712730132607 1.37273147849288 hap1 Brain - Hypothalamus hom 37 
-3.45020625780797 1.18533200381208 hap1 Brain - Hypothalamus hom 38 
-3.61103693406669 0.985810668100767 hap1 Brain - Hypothalamus hom 39 
-4.60517018598809 0 hap1 Brain - Hypothalamus hom 40 
-1.36046627633376 0.812257855129746 hap1 Brain - Hypothalamus hom 41 
-4.60517018598809 0 hap1 Brain - Hypothalamus hom 42 
-0.758614195344438 0.475371429738856 hap1 Brain - Hypothalamus hom 43 
-0.570751506996323 0.796705761206704 hap1 Brain - Hypothalamus hom 44 
-1.93529408140331 0.796764276230018 hap2 Brain - Amygdala het 1 
-1.2306095166114 1.12689741548906 hap2 Brain - Amygdala het 2 
-1.09158717166276 0.854886107611023 hap2 Brain - Amygdala het 3 
-2.41642059750677 1.69695118792728 hap2 Brain - Amygdala hom 4 
-0.975184099703771 0.516509361793386 hap2 Brain - Amygdala hom 5 
-4.60517018598809 0 hap2 Brain - Caudate (basal ganglia) het 6 
-4.60517018598809 0 hap2 Brain - Caudate (basal ganglia) het 7 
-4.60517018598809 0 hap2 Brain - Caudate (basal ganglia) het 8 
-4.60517018598809 0 hap2 Brain - Caudate (basal ganglia) het 9 
-1.72120397390227 1.07548128030902 hap2 Brain - Caudate (basal ganglia) het 10 
-2.70202205468788 1.16342600462607 hap2 Brain - Caudate (basal ganglia) het 11 
-3.18783283749423 1.05594737803958 hap2 Brain - Caudate (basal ganglia) het 12 
-1.40699203946488 0.48542701269273 hap2 Brain - Caudate (basal ganglia) het 13 
-1.87751485116197 0.935986612727037 hap2 Brain - Caudate (basal ganglia) het 14 
-2.05710440082911 1.1599569476391 hap2 Brain - Caudate (basal ganglia) het 15 
-4.60517018598809 0 hap2 Brain - Caudate (basal ganglia) het 16 
-3.28172961347489 1.16473022131648 hap2 Brain - Caudate (basal ganglia) hom 17 
-2.64643373422983 1.77404314601545 hap2 Brain - Caudate (basal ganglia) hom 18 
-2.93809040163993 1.31659399315286 hap2 Brain - Caudate (basal ganglia) hom 19 
-2.96028514861314 1.18901994150429 hap2 Brain - Caudate (basal ganglia) hom 20 
-2.94427746735641 1.40561781396035 hap2 Brain - Frontal Cortex (BA9) het 21 
-3.41394405787045 1.17429314258876 hap2 Brain - Frontal Cortex (BA9) hom 22 
-1.82465028645704 0.610451251569348 hap2 Brain - Frontal Cortex (BA9) hom 23 
-2.32519547889492 0.974453244714196 hap2 Brain - Frontal Cortex (BA9) hom 24 
-0.0114334599008076 0.246630953756596 hap2 Brain - Frontal Cortex (BA9) hom 25 
-2.73835203211445 1.30531030511388 hap2 Brain - Frontal Cortex (BA9) hom 26 
-3.24035798829041 1.28781584752539 hap2 Brain - Hippocampus het 27 
-3.12740315189855 1.29109745889288 hap2 Brain - Hippocampus het 28 
-3.19807533474438 1.37389171459244 hap2 Brain - Hippocampus hom 29 
-3.28828389936812 1.24441316535463 hap2 Brain - Hippocampus hom 30 
-4.60517018598809 0 hap2 Brain - Hippocampus hom 31 
-4.60517018598809 0 hap2 Brain - Hippocampus hom 32 
-4.60517018598809 0 hap2 Brain - Hippocampus hom 33 
-4.60517018598809 0 hap2 Brain - Hippocampus hom 34 
-3.08249674935387 1.31417447050384 hap2 Brain - Hippocampus hom 35 
-2.47020069079822 1.41087460604683 hap2 Brain - Hypothalamus hom 36 
-3.1010805356141 1.36869576597288 hap2 Brain - Hypothalamus hom 37 
-3.24746722228446 1.12654484449552 hap2 Brain - Hypothalamus hom 38 
-4.60517018598809 0 hap2 Brain - Hypothalamus hom 39 
-3.42959607400308 1.05586843920869 hap2 Brain - Hypothalamus hom 40 
-4.60517018598809 0 hap2 Brain - Hypothalamus hom 41 
-3.24002257386986 1.19536227038576 hap2 Brain - Hypothalamus hom 42 
-4.60517018598809 0 hap2 Brain - Hypothalamus hom 43 
-4.60517018598809 0 hap2 Brain - Hypothalamus hom 44 

我产生这个数字：使用此代码

：

replicate.plot = ggplot(data = replicate.plot.df, aes(factor(replicate), color = factor(haplotype))) 
replicate.plot = replicate.plot + geom_boxplot(aes(fill = factor(haplotype), 
lower = mean - std.dev, upper = mean + std.dev, middle = mean, ymin = mean - 3*std.dev, ymax = mean + 3*std.dev), 
position = position_dodge(width = 0), width = 0.5, alpha = 0.5, stat="identity") + facet_wrap(~tissue, ncol = 4, scales = "free_x") + 
scale_fill_manual(values = c("darkgreen","darkmagenta"),labels = c("haplotype.1","haplotype.2"), 
name = "haplotype allele")+scale_colour_manual(values = c("darkgreen","darkmagenta"), 
labels = c("haplotype.1","haplotype.2"),name = "haplotype allele") 

所以你可以看到我正在用haplotype字段对盒子着色。我想要做的是有两套不同的颜色：一对是hap1和hap2，它们是基因型het，另一对是hap1和hap2，它们是基因型hom，并且具有这两个层次的图例。

Answer 1

感兴趣的两个变量之间（单倍型和基因型）

replicate.plot.df$hapgeno<-interaction(replicate.plot.df$haplotype, 
    replicate.plot.df$genotype) 

，然后颜色的互动创建一个新变量基于该变量

ggplot(data = replicate.plot.df, aes(factor(replicate))) + 
    geom_boxplot(aes(fill = hapgeno, lower = mean - std.dev, upper = mean + std.dev, 
    middle = mean, ymin = mean - 3*std.dev, ymax = mean + 3*std.dev), 
    position = position_dodge(width = .5), width = 0.5, alpha = 0.5, stat="identity") +  
    facet_wrap(~tissue, ncol = 3, scales = "free_x") + 
    scale_fill_manual(values = c("darkgreen","darkmagenta","lightgreen","magenta"), 
    labels = c("haplotype.1.het","haplotype.2.het","haplotype.1.hom","haplotype.2.hom"), 
    name = "haplotype allele") 

，这让下面的情节