direction of bars in ggplot barplot with log scale axes

Question

I'm trying to create a bar plot of multiple data that has a log10 y-axis with nonzero values less than 1 like the image below (created in graphpad) based on the following data (dataframe = df):

No  Perc    Codon
1   72   ATA
2   12.7273  ATG
3   8.72727  GTG
4   0.727273     ATG
5   0.363636     GTG
6   0.363636     GTG
7   0.363636     GTG
8   0.363636     GTG
9   0.363636     GTG
10  0.363636     ATA
11  0.363636     ATA
12  0.363636     ATA
13  0.363636     ATA
14  0.363636     ATA
15  0.363636     ATA
16  0.363636     ATG
17  0.363636     ATG
18  0.363636     ATG
19  0.363636     ATG
20  0.363636     ATG

Using ggplot for the following data, I'm trying to create something similar based on other information from other questions to address my issues (to no avail).

ggplot(data=df,aes(x=No, y=Perc, color=Codon)) + geom_bar(stat="identity") + scale_y_log10( breaks=c(0.1, 1, 10, 100), limits=c(0.1, 100), position = "top") + coord_flip() + geom_segment( aes(x=No, xend=No, y=0.01, yend=Perc))

which produces the following image:

However, I would like the bar to continue in the same direction despite being less than 1. Moreover, is there a way that I can reposition the x-axis to the top of the graph and reorder the data such that the largest values are on the top as in the graphpad generated image?

I know that other similar questions have described simialr issues with the direction of the bars, but without solution.

Any help or advice for this novice would be much appreciated. Thanks!

Answer 1

Let me provide another answer, using the library(scales).

You were not putting the commands in the right order, and you cannot do a real log10 transformation, as values below 1 will became negative. Using library(scales) you can do a pseudo_log transformation. Here is my solution:

library(ggplot2)
library(scales)

df = data.frame("No" = seq_len(20),
                "Perc" = c(72.0, 12.7273,
                           8.72727, rep(0.363636, 17)),
                "Codon" = as.factor(c("ATA","ATG","GTG", "ATG",
                                      rep("GTG",5), rep("ATA",6),
                                      rep("ATG",5))))

breaks <- unique(c(seq(0,1,by = 0.1), 
    seq(1,10, 1), seq(10,100, 10)))
labs = c("","0.1",rep("",8),"1", 
    rep("",8), "10", rep("",8), "100")

gg  <- ggplot(data = df, aes(x = No, y = Perc, fill = Codon))
gg + geom_bar(stat = "identity") + 
coord_flip(ylim = c(0.1,100)) + scale_x_reverse() +
    scale_y_continuous(
        trans = pseudo_log_trans(base = 10),
        breaks = breaks, position = "right",
        labels = labs)

Hope it helps.

Oriol