Coloring ggplot by multiple factors

I have the following 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

And I produce this figure:

using this code:

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")

So as you can see I'm coloring the boxes by the haplotype field. What I'd like to do is have 2 different sets of colors: one pair for hap1 and hap2 which are of genotype het and another pair for hap1 and hap2 which are of genotype hom, and have the legend with these two levels as well.

Create a new variable for the interaction between the two variables of interest (haplotype and genotype)

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

and then color based on that variable

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")

and that makes the following plot