How to draw boxplot with each point and background color by R ?

Question

[takoyaki]

Hey everyone.

I failed to draw boxplot with each point by this R scripts and I want to know why.

m = data.frame( "A"=c(1,2,3), "B"=c(2,3,4) )

boxplot(m , xlab="Sample", ylab="value")

stripchart( m , vertical=TRUE, method="jitter", pch=c(21,22), col=c("red","blue"), bg=c("magenta","cyan"), cex=1.8, add=T)

From this script, I could draw boxplot and point itself, but background color is not my expectation.

I wanted to set background color magenta in group "A" and cyan in group "B".

Does anyone know why ? and how to draw like my expectation ?

Thanks.

[cpad0112]

m = data.frame( "A"=c(1,2,3), "B"=c(2,3,4) )
boxplot(m , xlab="Sample", ylab="value")
stripchart(list("A"=m$A, "B"=m$B), vertical=TRUE, method="jitter", col=c("red","blue"), cex=1.8, add=T, pch=16)

[takoyaki]

Thanks! That is what I wanted to draw !

[Arup Ghosh]

Like the following example?

[takoyaki]

no, background is "points" background. points in A should have magenta color and points in B should have cyan color.

[1769mkc]

Boxplot in ggplot2

[takoyaki]

now I tried to draw boxplot by default boxplot. but your comment is correct, so thanks

[Kevin Blighe]

Issue is resolved?

[takoyaki]

well, this is not resolved, but I'm giving up :)

[Kevin Blighe]

I see... I have posted the answer below.

Answer 1

[Kevin Blighe]

Here is how you can change the colour of the box-and-whiskers, and also the overlaid points.

Note the pairings for the colouring:

• Box-and-whisker plot: geom_boxplot() and scale_fill_manual()
• Scatter plot: geom_jitter() and scale_color_manual()

.

df <- data.frame(
  Group = c(rep('B-cell\nlymphocytes',50), rep('Natural\nkiller cells', 50)),
  log2(matrix(rexp(200, rate=.1), ncol=2)))
colnames(df) <- c('Group', 'Gene1', 'Gene2')

require(reshape2)
require(ggplot2)

df <- melt(df, id.vars = c('Group'))
colnames(df) <- c('Group', 'Gene', 'Expression')

ggplot(data = df, aes(x = Group, y = Expression)) +

    geom_boxplot(
      position = position_dodge(width=0.5),
      outlier.shape = 17,
      outlier.colour = 'red2',
      outlier.size = 0.1,
      aes(fill = Group)) +
    scale_fill_manual(values = c( 'red', 'royalblue')) + # for boxplot

    #Add the scatter points (treats outliers same as 'inliers')
    geom_jitter(
      position = position_jitter(width = 0.3),
      size = 3.0,
      aes(colour = Group)) +
    scale_color_manual(values = c('pink', 'skyblue')) + # for scatter plot dots

    # facet by Gene
    facet_wrap(~ Gene, ncol = 2) +

    #Set the size of the plotting window
    theme_bw(base_size=24) +

      #Modify various aspects of the plot text and legend
      theme(
        legend.position = 'none',
        legend.background = element_rect(),
        plot.title = element_text(angle = 0, size = 16, face = 'bold', vjust = 1),
        plot.subtitle = element_text(angle = 0, size = 16, face = 'bold', vjust = 1),
        plot.caption = element_text(angle = 0, size = 16, face = 'bold', vjust = 1),

        axis.text.x = element_text(angle = 45, size = 16, face = 'bold', hjust = 1.10),
        axis.text.y = element_text(angle = 0, size = 16, face = 'bold', vjust = 0.5),
        axis.title = element_text(size = 16, face = 'bold'),
        axis.title.x = element_text(size = 16, face = 'bold'),
        axis.title.y = element_text(size = 16, face = 'bold'),

        #Legend
        legend.key = element_blank(),       #removes the border
        legend.key.size = unit(1, 'cm'),        #Sets overall area/size of the legend
        legend.text = element_text(size = 14, face = 'bold'),   #Text size
        title=element_text(size = 14, face = 'bold'),

        #facet wrap
        strip.text.x = element_text(size = 14, face = 'bold'),
        strip.text.y = element_text(size = 14, face = 'bold', angle=0),
        strip.background = element_rect(fill = 'white'), 
        strip.text = element_text(size = 14, face = 'bold', colour = 'black'))+

    #Change the size of the icons/symbols in the legend
    guides(colour = guide_legend(override.aes = list(size = 2.5))) +

    #Set x- and y-axes labels
    xlab('Immune cell class') +
    ylab('Expression') +

    labs(title = 'Good morning',
      subtitle = 'Guten morgen',
      caption = 'Buongiorno')

Kevin

[takoyaki]

Thank you for long code ! I'm going to use as reference code. ggplot2 is so powerful.

[Kevin Blighe]

Indeed. I have been building up this code for a few years, adding to it each time. I now just copy-paste it when I need to generate plots like this. Happy to share it with you. In fact, that version (above) is a bit old, and I have already added more functionality to it ;)

[1769mkc]

your codes are lifesaver