[R] colours in ggplot2

[Antonello Preti]

Hi, I'm using ggplot2 to make a plot of the regression of a variable x (let
say, levels of depression),
on a variable y (let say, degree of social impairment),
by taking into account a binary factor (having had or not a past admission
to a psychiatric service),
and age of partecipants.

After some search in Internet I produced a code which is satisfying to me.
This site was very helpful: http://editerna.free.fr/wp/?p=266

However, I have a problem: no matter what I try, the figures always include
bluette and pink flamingo colours.
The figure is for an academic article, and I cannot afford the price of
having the plot printed in colours.

I've extracted the structure of the figure, and I understand that the
problem is in the scale_name "hue",
but I cannot figure out how to deal with it.

Any way to override the ggplot2 system of dealing with factors?

Here the codes and the sessionInfo
The code is a bit baroque, but this is the best I was able to do.


Thank you in advance,
Antonello Preti



######## code for exemplification

### the dataset

df <- structure(list(Social_impairment = c(2.83, 3.08, 2.75, 2.08,
2.92, 1.75, 3.5, 2.33, 2.91, 2.5, 3.25, 2.64, 3.25, 2.83, 2.08,
2.25, 2.17, 2.42, 2.58, 2.42, 2.58, 2.42, 3, 3, 2.83, 2.67, 3.58,
1.58, 2.83, 2.83, 2.67, 3.17, 2.42, 1.92, 2.92, 2.5, 2.42, 2.42,
2.58, 2.42, 3.33, 3, 3.17, 2.17, 2.58, 2.67, 2.58, 3.75, 2.5,
2.08, 2.25, 3.25, 3.17, 2.91, 2.08, 2.25, 3.08, 2.91, 3.08, 2.92,
1.83, 2.5, 2.5, 2.83, 2.67, 3.33, 2.83, 3.33, 2.92, 3), Levels_Depression =
c(1.3,
1.71, 3.08, 0.48, 0.51, 0.71, 1.37, 0.2, 1.21, 1.07, 2.8, 1.24,
0.46, 0.97, 0.81, 1.13, 1.58, 3.12, 1.8, 1.54, 1.02, 0.32, 2.63,
1.39, 1.34, 2.37, 2.6, 1.11, 1.59, 2.17, 1.99, 0.59, 0.76, 0.23,
2.22, 1.98, 0.41, 0.32, 0.37, 1.11, 2.29, 0.97, 1.61, 1.27, 1.22,
2.38, 1.28, 1.21, 0.93, 2.3, 0.8, 2.1, 2.86, 2.47, 2.34, 2.67,
0.31, 0.88, 1.84, 0.23, 2.41, 0.56, 2.03, 1.11, 0.12, 2.39, 0.34,
2.08, 1.01, 1.51), Age = c(66, 59, 49, 70, 42, 55, 28, 41, 69,
65, 40, 21, 18, 77, 28, 40, 47, 37, 47, 39, 32, 33, 42, 28, 59,
49, 29, 41, 22, 29, 53, 39, 55, 61, 30, 49, 43, 46, 18, 36, 34,
17, 42, 37, 37, 54, 48, 23, 71, 42, 52, 83, 19, 47, 23, 80, 43,
38, 47, 80, 36, 73, 74, 51, 76, 14, 65, 39, 17, 73), Past_Admissions = c(1,
1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1,
1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0,
0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0,
1, 0, 1, 0, 0, 1)), .Names = c("Social_impairment", "Levels_Depression",
"Age", "Past_Admissions"), row.names = c(NA, 70L), class = "data.frame")

dim(df)
head(df)
str(df)
summary(df)


### call the library

library(ggplot2)


#### the plot


#### Levels_Depression on Social_impairment by Past_Admissions (yes/no)
#### linear model
#### radius of the bubbles proportional to age


#### background elimination

p1 <- ggplot(data = df, aes(x =Levels_Depression, y = Social_impairment,
group = as.factor(Past_Admissions), col = as.factor(Past_Admissions))) +
  geom_point(aes(size = Age)) + geom_smooth(method = "lm") + xlab("Levels
of depression") + ylab("Social impairment") +
  scale_colour_discrete("History of \npast admissions\nto a psychiatric
service", labels = c("No", "Yes"))

p1 + theme(panel.grid.major = element_blank(), panel.grid.minor =
element_blank(),
    panel.background = element_blank(), axis.line = element_line(colour =
"black"))


### change of then axes' ticks

p1 + theme(panel.grid.major = element_blank(), panel.grid.minor =
element_blank(),
    panel.background = element_blank(), axis.line = element_line(colour =
"black"),
    axis.text = element_text(color = "black", size = 12, face = "italic"))


### after saving, dev.off()
###


#### Age on Social_impairment by Past_Admissions (yes/no)
#### linear model
#### radius of the bubbles proportional to Levels_Depression



#### background elimination

p2 <- ggplot(data = df, aes(x =Age , y = Social_impairment, group =
as.factor(Past_Admissions), col = as.factor(Past_Admissions))) +
  geom_point(aes(size = Levels_Depression)) + geom_smooth(method = "lm")
+xlab("Age of participants") + ylab("Social impairment") +
  scale_colour_discrete("History of \npast admissions\nto a psychiatric
service", labels = c("No", "Yes"))

p2 + theme(panel.grid.major = element_blank(), panel.grid.minor =
element_blank(),
    panel.background = element_blank(), axis.line = element_line(colour =
"black"))


### change of then axes' ticks

p2 + theme(panel.grid.major = element_blank(), panel.grid.minor =
element_blank(),
    panel.background = element_blank(), axis.line = element_line(colour =
"black"),
    axis.text = element_text(color = "black", size = 12, face = "italic"))


### after saving, dev.off()
###


########################
#### paired plots
########################

library(gridExtra)

grid.arrange(p1, p2, ncol = 2)



########################
### sessionInfo()
########################

R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
[3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.1252

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] gridExtra_0.9.1 ggplot2_0.9.3.1

loaded via a namespace (and not attached):
 [1] colorspace_1.2-4   dichromat_2.0-0    digest_0.6.4
gtable_0.1.2
 [5] labeling_0.2       MASS_7.3-33        munsell_0.4.2
plyr_1.8
 [9] proto_0.3-10       RColorBrewer_1.0-5 reshape2_1.2.2
scales_0.2.3
[13] stringr_0.6.2

	[[alternative HTML version deleted]]