Transform y axis in bar plot using scale_y_log10()

Question

Using the data.frame below, I want to have a bar plot with y axis log transformed.

I got this plot

using this code

ggplot(df, aes(x=         


        

Answer 1

If you need bars flipped, maybe calculate your own log10(y), see example:

library(ggplot2)
library(dplyr)

# make your own log10
dfPlot <- df %>% 
  mutate(ymin = -log10(ymin),
         ymax = -log10(ymax),
         ymean = -log10(ymean))

# then plot
ggplot(dfPlot, aes(x = id, y = ymean, fill = var, group = var)) +
  geom_bar(position = "dodge", stat = "identity",
           width = 0.7,
           size = 0.9)+
  geom_errorbar(aes(ymin = ymin, ymax = ymax),
                size = 0.25,   
                width = 0.07,
                position = position_dodge(0.7)) +
  scale_y_continuous(name = expression(-log[10](italic(ymean)))) + 
  theme_bw() 

Answer 2

Firstly, don't do it! The help file from ?geom_bar says:

A bar chart uses height to represent a value, and so the base of the bar must always be shown to produce a valid visual comparison. Naomi Robbins has a nice article on this topic. This is why it doesn't make sense to use a log-scaled y axis with a bar chart.

To give a concrete example, the following is a way of producing the graph you want, but a larger k will also be correct but produce a different plot visually.

k<- 10000  

ggplot(df, aes(x=id, y=ymean*k , fill=var, group=var)) +
  geom_bar(position="dodge", stat="identity",
           width = 0.7,
           size=.9)+
  geom_errorbar(aes(ymin=ymin*k,ymax=ymax*k),
                size=.25,   
                width=.07,
                position=position_dodge(.7))+
  theme_bw() + scale_y_log10(labels=function(x)x/k)

k=1e4

k=1e6

Answer 3

As @Miff has written bars are generally not useful on a log scale. With barplots, we compare the height of the bars to one another. To do this, we need a fixed point from which to compare, usually 0, but log(0) is negative infinity.

So, I would strongly suggest that you consider using geom_point() instead of geom_bar(). I.e.,

ggplot(df, aes(x=id, y=ymean , color=var)) +
  geom_point(position=position_dodge(.7))+
  scale_y_log10("y",
                breaks = trans_breaks("log10", function(x) 10^x),
                labels = trans_format("log10", math_format(10^.x)))+
  geom_errorbar(aes(ymin=ymin,ymax=ymax),
                size=.25,   
                width=.07,
                position=position_dodge(.7))+
  theme_bw()

If you really, really want bars, then you should use geom_rect instead of geom_bar and set your own baseline. That is, the baseline for geom_bar is zero but you will have to invent a new baseline in a log scale. Your Plot 1 seems to use 10^-7.

This can be accomplished with the following, but again, I consider this a really bad idea.

ggplot(df, aes(xmin=as.numeric(id)-.4,xmax=as.numeric(id)+.4, x=id, ymin=10E-7, ymax=ymean, fill=var)) +
  geom_rect(position=position_dodge(.8))+
  scale_y_log10("y",
                breaks = trans_breaks("log10", function(x) 10^x),
                labels = trans_format("log10", math_format(10^.x)))+
  geom_errorbar(aes(ymin=ymin,ymax=ymax),
                size=.25,   
                width=.07,
                position=position_dodge(.8))+
  theme_bw()