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#Load required packages
require(agricolae)
require(ggplot2)
require(plotrix)

#Data
cuke<-structure(list(Treatment = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L
), .Label = c("Con", "ConM", "Eth", "EthM"), class = "factor"), 
Day = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 
6L, 6L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 
9L, 9L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 
12L, 12L, 12L, 12L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 6L, 6L, 6L, 
6L, 6L, 9L, 9L, 9L, 9L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 
12L, 12L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 
6L, 6L, 6L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 
9L, 9L, 9L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 
12L, 12L, 12L, 12L, 12L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 6L, 
6L, 6L, 6L, 6L, 9L, 9L, 9L, 9L, 12L, 12L, 12L, 12L, 12L, 
12L, 12L, 12L, 12L), Hue = c(123.79, 126.82, 123.24, 122.5, 
125.44, 124.11, 125.99, 122.7, 119.09, 124.96, 125.46, 124.27, 
125.92, 126.29, 125.57, 126.52, 125.38, 126.98, 125.22, 126.02, 
126.01, 124.73, 124.13, 127.15, 126.78, 126.92, 127.15, 126.44, 
126.59, 126.63, 123.87, 121.96, 123.2, 123.43, 122.98, 124.48, 
123.74, 123.96, 124.32, 124.32, 125.04, 126.46, 126.66, 125.51, 
121.44, 123.19, 124.46, 124.57, 122.62, 123.56, 122.81, 124.29, 
124.16, 122.25, 123.14, 124.1, 124.02, 123.64, 124.98, 124.8, 
123.19, 124.46, 124.57, 122.62, 123.56, 122.81, 124.29, 124.16, 
122.25, 123.14, 124.1, 124.02, 123.64, 124.98, 123.79, 126.82, 
122.5, 125.44, 125.99, 122.7, 119.09, 123.57, 122.82, 125.18, 
119.55, 123.26, 119.37, 118.79, 115.25, 115.67, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, 123.99, 123.89, 124.76, 121.45, 123.06, 
125.55, 127, 123.92, 124.29, 120.91, 125.69, 124.25, 124.11, 
123.67, 123.21, 123.56, 126.69, 126.14, 125.37, 126.76, 127.41, 
122.39, 122.65, 122.24, 123.11, 125.63, 123.21, 123.39, 123.08, 
123.54, 124.69, 123.21, 121.3, 121.82, 123.9, 123.42, 123.92, 
119.89, 120.68, 119.42, 119.57, 119.85, 123.17, 125.96, 125.75, 
121.14, 125.01, 124.03, 124.56, 121.84, 120.25, 118.74, 121.94, 
117.09, 119.7, 111.07, 118.03, 119.32, 118.92, 121.07, 114.65, 
111.78, 113.44, 115.05, 112.74, 115.45, 121.8, 120.91, 122.49, 
123.99, 118.47, 123.31, 116.42, 114.15, 123.99, 123.89, 121.45, 
123.06, 127, 123.92, 124.29, 119.01, 116.52, 113.18, 113.56, 
107.57, 107.52, 112.53, 117.23, 117.32, 95.86572469, 101.1846093, 
101.8936238, 106.3913542, 105.6866304, 99.76811364, 107.0792098, 
108.0885293, 95.76880979)), .Names = c("Treatment", "Day", 
"Hue"), class = "data.frame", row.names = c(NA, -198L))

#returns a list with the aov by day in a list
cukebyday.aov <- dlply(cuke, .(Day), function(x) aov(Hue ~ Treatment, data=x))


#Returns data frame with mean, SEM, grouping factor, UCI, LCI
lsd <- ldply(cukebyday.aov, function(x) LSD.test(x, "Treatment"))

p <- ggplot(lsd, aes(Day, means, group=trt))+
geom_line(aes())+
geom_point(aes(shape = trt), size=4) +
geom_errorbar(aes(ymax=UCI, ymin=LCI), width=0.5)+
opts(axis.text.x=theme_text(angle=-45, hjust=0, size=9))+
geom_text(aes(x=Day, y=means, label=M, hjust=2, vjust=2))+
theme_bw()

p