How to plot several boxplots by group in r?

Question

ID <- 1:10 
group <- c(1,1,1,2,2,2,3,3,3,3)
var1 <- c(6:15) 
var2 <- c(7:16) 
var3 <- c(6:11, NA, NA, NA, NA)
var4 <- c(4:9, NA, NA, NA, NA) 
data <- data.frame(ID, group, var1, var2, var3, var4)

library(dplyr)
 data %>% group_by(group) %>% boxplot(var1, var2)

The last line does not work as i wish. The idea is to get 4 boxplots in one graphic. Two for each variable. Maybe i need to use ggplot2?

You mean like boxplot(value~group+variable, reshape2::melt(data, 1:2)) (May need install.packages("reshape2") beforehand)? — lukeA
– lukeA, Commented May 9, 2016 at 12:55

Community · Accepted Answer · 2017-05-23 10:28:15Z

13

You need to reorganize the data if you want to get both variables in the same plot. Here is a ggplot2 solution:

# load library
  library(ggplot2)
  library(tidyr)
  library(ggthemes)


# reorganize data
  df <- gather(data, "ID","group") 

#rename columns 
  colnames(df) <- c("ID","group","var","value")

# plot
  ggplot(data=df) + 
    geom_boxplot( aes(x=factor(group), y=value, fill=factor(var)), position=position_dodge(1)) +
    scale_x_discrete(breaks=c(1, 2, 3), labels=c("A", "B", "C")) +
    theme_minimal() +
    scale_fill_grey()

Making boxplots with the same width is a whole different question (solution here), but one simple alternative would be like this:

# recode column `group` in the `data.frame`.
  df <- transform(df, group = ifelse(group==1, 'A', ifelse(group==2, 'B', "C")))

# plot
  ggplot(data=df) + 
  geom_boxplot( aes(x=factor(var), y=value, fill=factor((var))), position=position_dodge(1)) +
  geom_jitter(aes(x=factor(var), y=value, color=factor((var)))) +
  facet_grid(.~group, scales = "free_x") +
  theme_minimal()+
  scale_fill_grey() +
  theme(axis.text.x=element_blank(),
        axis.title.x=element_blank(),
        axis.ticks=element_blank())

edited May 23, 2017 at 10:28

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answered May 9, 2016 at 12:58

rafa.pereira

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6 Comments

SDahm Over a year ago

Thank you for this easy solution. I still have some "style" questions, because my actual dataset is a little bit more complicated.

SDahm Over a year ago

ID <- 1:10 group <- c(1,1,1,2,2,2,3,3,3,3) var1 <- c(6:15) var2 <- c(7:16) var3 <- c(6:11, NA, NA, NA, NA) var4 <- c(4:9, NA, NA, NA, NA) data <- data.frame(ID, group, var1, var2, var3, var4) # load library library(ggplot2) library(tidyr) # reorganize data df <- gather(data, "ID","group") #rename columns colnames(df) <- c("ID","group","var","value") # plot ggplot(data=df) + geom_boxplot( aes(x=factor(group), y=value, fill=factor(var))) + geom_jitter(aes(x=factor(group), y=value))

SDahm Over a year ago

# set space between the boxes, they are to close together, especially for the jitter # set all boxes the same width; Because of missings the third block is different # change colour to greyscales or black and white pattern # name the groups (1,2,3) --> "A","B","C"

rafa.pereira Over a year ago

Here you will find a solution for how to make boxplots with the same width. I've addressed your other points in the edit to my question

SDahm Over a year ago

Thanks, this looks very nice :) When i add geom_jitter unfurtunately the dots are outside the boxes and i can not find a solution to change that. I tried to set width or as in your example position=position_dodge. Width does not change anything. Position made it one line in between.

|

BenBarnes · Accepted Answer · 2016-05-09 13:10:51Z

5

You might try melting the data frame (mentioned in comment by @lukeA) first and then sticking to base graphics. ggplot2 or lattice are other good options.

library(reshape2)

DF <- melt(data, id.vars = c("ID", "group"), measure.vars = c("var1", "var2"))

boxplot(value ~ group + variable, DF)

Alternate lattice code, also using DF:

bwplot(~ value | variable + group, data = DF)

Alternate ggplot2 code, also using DF:

ggplot(DF, aes(x = factor(group), y = value, fill = variable)) + geom_boxplot()

edited May 9, 2016 at 13:10

answered May 9, 2016 at 12:57

BenBarnes

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Comments

Christoph · Accepted Answer · 2022-03-15 17:06:35Z

Although quite late, a found a great base-R solution here

# Create some data, e.g. from https://en.wikipedia.org/wiki/One-way_analysis_of_variance#Example
df <- as.data.frame(matrix(c(6, 8, 13, 8, 12, 9, 4, 9, 11, 5, 11, 8, 3, 6, 7, 4, 8, 12),ncol = 3, byrow = TRUE))
df <- reshape(data = df, direction = "long", idvar=1:3, varying=1:3, sep = "", timevar = "Treatment")
df$Treatment <- as.factor(df$Treatment)
rownames(df) <- NULL

par(mfrow = c(2, 1))
par(mar=c(1,4,4,2) + 0.1) # mar=c(b,l,t,r)
boxplot(V ~ Treatment, data = df, xlab = NULL, xaxt = "n",
        ylab = "V", main = "One-way anova with 3 different levels of one factor")
stripchart(V ~ Treatment,     # Points
           data = df,         # Data
           method = "jitter", # Random noise
           pch = 19,          # Pch symbols
           col = 4,           # Color of the symbol
           vertical = TRUE,   # Vertical mode
           add = TRUE)        # Add it over

par(mar=c(5,4,0,2) + 0.1)
boxplot(V ~ Treatment, data = df, xlab = "Treatment",
        ylab = "V", main = NULL)
stripchart(V ~ Treatment,     # Points
           data = df,         # Data
           method = "overplot", # Random noise
           pch = 19,          # Pch symbols
           col = 4,           # Color of the symbol
           vertical = TRUE,   # Vertical mode
           add = TRUE)        # Add it over
par(mfrow = c(1, 1))

Result:

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