[R] colours in ggplot2

Mon Feb 23 12:44:01 CET 2015

Dear Antonello,

How about this? Obviously, you can change the background colours for the confidence levels (deprespal) and for the regression lines, etc.
Surely, many in the list can improve on my rough and ready solution.

deprespal=c("#CCCCCC","#999999")
p2 <- ggplot(data = df, aes(x =Levels_Depression, y = Social_impairment, group = as.factor(Past_Admissions),fill = as.factor(Past_Admissions) )) +
    geom_point(aes(size = Age)) + geom_smooth(method = "lm", col="black") + xlab("Levels of depression") + ylab("Social impairment") +
    scale_fill_manual(values=deprespal) +
    scale_colour_discrete("History of \npast admissions\nto a psychiatric service", labels = c("No", "Yes"))
p2

Regards,

José

Prof. José Iparraguirre
Chief Economist
Age UK

Age UK
Tavis House, 1- 6 Tavistock Square
London, WC1H 9NB

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Antonello Preti
Sent: 20 February 2015 12:54
To: r-help at r-project.org
Subject: [R] colours in ggplot2

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

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