[R] Color-coding data points in complex dotplot (ggplot2)

Sat Apr 6 01:53:44 CEST 2019

Dear R-List members,

I produced a dot plot (see attachment 1) on 6 different treatments (trees
under 6 different conditions; in column " Location.Treatment " in my raw
data). For each of these " Location.treatment" categories, I calculated a
mean value and the SE for a specific compound (%CT).

I am able to produce a plot where all the 6 treatments (in column "
Location.Treatment") are separated (see code and Fig. 1) so that each of two
"con" and "exp" treatments (in the column "treatment") are nested within one
of the three locations (High, mid, low; in the column "Location") (see plot
that the code produces). This is the plot structure I want.

Now I would like to assign colors to the raw data points ( the "point cloud"
next to each mean +SE value). Each of these points stems from a different
"Genotype" and I would like to color code the points with regard to the
genotypes (e.g. all points from Genotype A should be green, all points from
Genotype B should be red etc.) I would like to use my own specified colors
in the code (not the standard palette).

I tried did the following (without success)

1.      I added "aes(color=Genotype,.." into "geom_point(..)"

2.      I added my specific colors to "scale_color_manual"

scale_color_manual(labels=c("Control","Damaged"),values=c("red","black","#06
7c43","#89b651","#dc5b09","#e4a710","#92c5de","grey","#1d71b4","#7873a3"....
..

However, if I do that my "nested" plot structure disappears (i.e. I cannot
visually differentiate between "con" and "exp" treatments nested within mid
/high/. See Fig. 2)

Basically, all I want is to produce a plot that looks like the one from my
actual code( Fig.1) but where the individual data points are colored
according to "Genotypes"

Below is my code and my raw data.

Help is very much appreciated!

Thanks a lot,

Mike

#CODE-----------------------------------------------------

require(ggplot2)

#REMOVE START FOR ANALYSIS

dta<-subset(dta_complete,Time=="Stop")

dta

#Calculation of SE

data_summary <- function(x) {

  m <- mean(x)

  ymin <- m-sd(x)/sqrt(length(x))

  ymax <- m+sd(x)/sqrt(length(x))

  return(c(y=m,ymin=ymin,ymax=ymax))

}

pd1 = position_dodge(0.5)

plot_CT<- ggplot(dta, aes(x=Location, y=CT,
colour=Treatment,shape=Treatment)) +

  stat_summary(fun.data=data_summary, position=pd1, geom="errorbar",
width=0.05) +

  stat_summary(fun.data=data_summary, position=pd1, geom="point", size=2) +

  geom_point(position=position_jitterdodge(dodge.width=0.8, jitter.height=0,
jitter.width=0.2),

             alpha=0.7) +

  labs(title="", x="", y = "CT (% dw)")+

  scale_color_manual(labels=c("Control",
"Damaged"),values=c("red","black"),guide = guide_legend(reverse = TRUE) )+

  scale_shape_manual(labels=c("Control", "Damaged"),name="Treatment",values
= c(16,16),guide = guide_legend(reverse = TRUE) )+

  #Style of background

  theme_classic()+

  #Change title

  theme(plot.title = element_text(color="black", size=17, face="bold"))+

  #Font size axis

  theme(axis.text=element_text(size=12),

        axis.title=element_text(size=17))+

  scale_x_discrete("Location",labels = c("Low", "Mid", "High"),expand=c(0.1,
0.5))+

  coord_flip()

plot_CT

#DATA-----------------------------------------------------------------------
-----------------

structure(list(Location = structure(c(2L, 3L, 1L, 2L, 3L, 1L,

2L, 3L, 1L, 2L, 3L, 1L, 2L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L,

1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L,

2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,

3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L,

1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L,

3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L,

1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L,

2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,

3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L,

1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L,

2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,

3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L), .Label = c("High", "Low", "Mid"

), class = "factor"), Treatment = structure(c(2L, 2L, 2L, 1L,

1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L,

1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L,

2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L,

1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L,

1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L,

2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L,

2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L,

1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,

2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L,

2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L,

1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,

2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L), .Label = c("Con", "Exp"

), class = "factor"), Time = structure(c(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, 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, 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), .Label = c("Start", "Stop"

), class = "factor"), Genotype = structure(c(7L, 7L, 7L, 7L,

7L, 7L, 4L, 4L, 4L, 4L, 4L, 4L, 6L, 6L, 6L, 6L, 6L, 2L, 2L, 2L,

2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 8L, 8L, 8L, 8L, 8L, 8L, 1L,

1L, 1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L,

4L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 6L, 6L, 6L,

6L, 6L, 6L, 8L, 8L, 8L, 8L, 8L, 8L, 5L, 5L, 5L, 5L, 5L, 5L, 7L,

7L, 7L, 7L, 7L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L, 5L, 5L,

1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L,

4L, 4L, 2L, 2L, 2L, 2L, 2L, 2L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L,

7L, 7L, 7L, 7L, 6L, 6L, 6L, 6L, 6L, 6L, 8L, 8L, 8L, 8L, 8L, 8L,

2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L,

1L, 1L, 5L, 5L, 5L, 5L, 5L, 5L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L,

8L, 8L, 8L, 8L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("A", "B",

"C", "D", "E", "F", "G", "H"), class = "factor"), Time.Location =
structure(c(5L,

6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 4L, 5L, 6L, 4L,

5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L,

6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L,

4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L,

5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L,

6L, 4L, 5L, 6L, 4L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L,

5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L,

6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L,

4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L,

5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L,

6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L,

4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L, 5L, 6L, 4L), .Label = c("StartHigh",

"StartLow", "StartMid", "StopHigh", "StopLow", "StopMid"), class =
"factor"),

    Location.Treatment = structure(c(4L, 6L, 2L, 3L, 5L, 1L,

    4L, 6L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L,

    5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L,

    6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L,

    5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L,

    6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L,

    5L, 1L, 4L, 6L, 2L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L,

    2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L,

    1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L,

    2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L,

    1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L,

    2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L,

    1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L, 2L, 3L, 5L, 1L, 4L, 6L,

    2L, 3L, 5L, 1L), .Label = c("HighCon", "HighExp", "LowCon",

    "LowExp", "MidCon", "MidExp"), class = "factor"), CT = c(4.61538,

    3.96739, 7.34797, 3.58108, 2.89655, 2.7993, 10.56122, 10.68396,

    15.57252, 6.79245, 9.23469, 9.18, 1.1087, 4.26136, 1.14504,

    2.20238, 3.15789, 9.54082, 11.05263, 15.84783, 10.48986,

    12.62195, 15.12931, 5.51471, 8.20313, 11.85811, 3.38115,

    7.5, 9.69512, 8.64407, 11.30597, 14.42797, 8.8125, 11.82482,

    11.53061, 6.97674, 9.62766, 10.88028, 5.50403, 9.73558, 8.56419,

    11.84524, 16.34892, 18.15789, 10.58036, 14.80932, 12.06081,

    12.96992, 9.86014, 12.45652, 6.625, 6.93396, 9.10714, 3.66142,

    9.19811, 10.88346, 2.88851, 6.85096, 10.27778, 8.29787, 13.00885,

    14.38017, 7.5, 11.77734, 13.84615, 2.22772, 5.28, 5.25641,

    1.0514, 2.73256, 4.11111, 11.39098, 11.10236, 13.00781, 7.95259,

    10.15748, 13.16327, 8.90625, 10.04587, 13.625, 6.27049, 9.27966,

    10.94037, 5.80189, 7.76978, 7.34266, 3.80952, 3.75, 7.29545,

    10.45872, 16.83206, 5.95238, 7.70833, 10.92391, 11.03659,

    14.39338, 14.88281, 8.22917, 11.63603, 14.7561, 11.9469,

    14.65649, 16.84615, 8.37209, 13.27982, 13.69128, 7.77778,

    12.59124, 12.32955, 7.00472, 8.41121, 7.22222, 9.43878, 10.33613,

    14.16667, 9.60526, 8.77232, 11.91589, 7.01786, 12.29592,

    11.83673, 8.55634, 11.17347, 12.68836, 2.7551, 6, 7.21374,

    2.52101, 4.03846, 4.80634, 5.49569, 4.78723, 6.02273, 3.04511,

    3.59244, 2.48239, 1.54412, 5.74219, 7.68595, 1.33065, 2.625,

    4.42164, 9.66942, 11.875, 17.91667, 10.81731, 13.05288, 16.23853,

    11.93662, 14.31818, 14.09396, 7.82374, 15.5042, 10.86207,

    6.87023, 11.69492, 12.65957, 3.48684, 5.29018, 7.89474, 10.53309,

    17.05479, 16.63866, 7.43119, 12.06522, 12.05607, 6.14865,

    10.44, 14.69512, 9.24757, 9.04018, 12.38255, 2.22222, 3.90756,

    5.85616, 2.23958, 3.8125, 3.01056, 11.60256, 12.22222, 11.8007,

    7.76316, 10.08197, 12.78777, 9.20455, 12.1875, 16.59449,

    6.82331, 10.91518, 11.5748)), row.names = 192:381, class = "data.frame")