Transform y axis in bar plot using scale_y_log10() - r

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=id, y=ymean , fill=var, group=var)) +
geom_bar(position="dodge", stat="identity",
width = 0.7,
size=.9)+
geom_errorbar(aes(ymin=ymin,ymax=ymax),
size=.25,
width=.07,
position=position_dodge(.7))+
theme_bw()
to log transform y axis to show the "low" level in B and D which is close to zero, I used
+scale_y_log10()
which resulted in
Any suggestions how to transform y axis of the first plot?
By the way, some values in my data is close to zero but none of it is zero.
UPDATE
Trying this suggested answer by #computermacgyver
ggplot(df, aes(x=id, y=ymean , fill=var, group=var)) +
geom_bar(position="dodge", stat="identity",
width = 0.7,
size=.9)+
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()
I got
DATA
dput(df)
structure(list(id = structure(c(7L, 7L, 7L, 1L, 1L, 1L, 2L, 2L,
2L, 6L, 6L, 6L, 5L, 5L, 5L, 3L, 3L, 3L, 4L, 4L, 4L), .Label = c("A",
"B", "C", "D", "E", "F", "G"), class = "factor"), var = structure(c(1L,
2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,
3L, 1L, 2L, 3L), .Label = c("high", "medium", "low"), class = "factor"),
ymin = c(0.189863418, 0.19131948, 0.117720496, 0.255852069,
0.139624146, 0.048182771, 0.056593774, 0.037262727, 0.001156667,
0.024461299, 0.026203592, 0.031913077, 0.040168571, 0.035235902,
0.019156667, 0.04172913, 0.03591233, 0.026405094, 0.019256055,
0.011310755, 0.000412414), ymax = c(0.268973856, 0.219709677,
0.158936508, 0.343307692, 0.205225352, 0.068857143, 0.06059596,
0.047296296, 0.002559633, 0.032446541, 0.029476821, 0.0394,
0.048959184, 0.046833333, 0.047666667, 0.044269231, 0.051,
0.029181818, 0.03052381, 0.026892857, 0.001511628), ymean = c(0.231733739333333,
0.204891473333333, 0.140787890333333, 0.295301559666667,
0.173604191666667, 0.057967681, 0.058076578, 0.043017856,
0.00141152033333333, 0.0274970166666667, 0.0273799226666667,
0.0357511486666667, 0.0442377366666667, 0.0409452846666667,
0.0298284603333333, 0.042549019, 0.0407020586666667, 0.0272998796666667,
0.023900407, 0.016336106, 0.000488014)), class = c("tbl_df",
"tbl", "data.frame"), row.names = c(NA, -21L), .Names = c("id",
"var", "ymin", "ymax", "ymean"))

Answer 1

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()

Answer 2

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 3

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