Simple-plots-in-R/Box & whisker plots at master · FEMLab/Simple-plots-in-R · GitHub

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# Box and whisker plots

# Libraries needed:

library(ggplot2)
library(grid)

# example data: (scatter.txt)

	Week	pH	Treatment	Location
1	0	5.58	Zero	Soil
2	2	5.245	Zero	Rhizo
3	4	5	Zero	Soil
4	5	4.9025	Zero	Soil
5	0	4.9	Zero	Rhizo
6	2	4.85	Zero	Rhizo
7	4	4.845	Zero	Rhizo
8	5	5.1375	Zero	Soil
9	0	5.17	High	Soil
10	2	5.0425	High	Soil
11	4	5.3025	High	Rhizo
12	5	5.155	High	Rhizo
13	6	5.6275	High	Soil
14	0	5.8	High	Soil
15	2	5.9	High	Soil
16	4	6.0	High	Rhizo
17	5	7.2	High	Rhizo
18	6	6.5	High	Soil

# read in data

d <- read.table("scatter.txt", sep = "\t", row.names=1, header=T)

## plot using ggplot here
## aes(factor(what you want on x axis), whatyouwantonYaxis, fill=factor(treatmentForEg))

ggplot(d, aes(as.factor(Week), pH, fill = factor(Treatment))) +

  ## + geom_boxplot so it knows what type of plot

  geom_boxplot() +

  ## scale_fill_manual to give different from default colour
  ## name argument gives legend title
  ## colours: http://sape.inf.usi.ch/quick-reference/ggplot2/colour

  scale_fill_manual(name = "Lime Treatment", values = c("royalblue2", "green4")) +

  ## theme_bw() to make background white

  theme_bw() +

  ## specify labels for axes and plot title if required

  labs(x="Sampling Day", y="pH") +

  ## change text size and placing of axes and titles
  ## ensure , at end of each line
  ## legend.key.size changes size of legend and required 'grid' package to be loaded for unit() to work

  theme(axis.text.x=element_text(size=12, vjust=0.5),
        axis.text.y=element_text(size=12, vjust=0.5),
        axis.title.x=element_text(size=16, vjust=0.25, face = "bold"),
        axis.title.y=element_text(size=16, vjust=1, face = "bold"),
        legend.title=element_text(size=16, vjust=1),
        legend.text=element_text(size=15, vjust=0.5),
        legend.key.size=unit(1.5, "cm")
  )


## Links used to make this code:
## for most:
## http://docs.ggplot2.org/0.9.3.1/geom_boxplot.html
## For changing themes, usual cheat sheet and this:
## http://docs.ggplot2.org/current/theme.html
## how to change colours:
## http://stackoverflow.com/questions/8320462/ggplot2-how-to-adjust-fill-colour-in-a-boxplot-and-change-legend-text