Log10 Y 轴从 0 开始

Question

I created a bar plot to show differences in water accumulation on different sites and layers. Because one value is way higher than the other ones I want to set the y-axis on log10 scale. It all works but the result looks rather unintuitive. is it possible to set the limit of the y-axis to 0 so the bar with the value 0.2 is not going downwards?

Here is the code I used:

p2 <- ggplot(data_summary2, aes(x= Site, y= small_mean, fill= Depth, Color= Depth))+
  geom_bar(stat = "identity", position = "dodge", alpha=1)+
  geom_errorbar(aes(ymin= small_mean - sd, ymax= small_mean + sd),
                position = position_dodge(0.9),width=0.25,   alpha= 0.6)+
  scale_fill_brewer(palette = "Greens")+
  geom_text(aes(label=small_mean),position=position_dodge(width=0.9), vjust=-0.25, hjust= -0.1, size= 3)+
  #geom_text(aes(label= Tukey), position= position_dodge(0.9), size=3, vjust=-0.8, hjust= -0.5, color= "gray25")+
  theme_bw()+
  theme(legend.position = c(0.2, 0.9),legend.direction = "horizontal")+
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
  labs(fill="Depth [cm]")+
  theme(axis.text.x = element_text(angle = 25, size =9, vjust = 1, hjust=1))+
  scale_x_discrete(labels= c( "Site 1\n(Hibiscus tillaceus)","Site 2 \n(Ceiba pentandra)","Site 3 \n(Clitoria fairchildiana)","Site 4 \n(Pachira aquatica)"))+
  #theme(legend.position = c(0.85, 0.7))+
  labs(x= "Sites\n(Type of Tree)", y= "µg Deep-Water/ g rhizosphere soil", title = "Average microbial Deep-water incorporation per Site", subtitle = "Changes over Time and Depth")+
  facet_grid(.~Time, scale = "free")
p2 + scale_y_continuous(trans = "log10")

This is what the plot looks like:

Answer 1

On a log scale there is no 0 , therefore the only sensible place for bars to start from is y = log10(0) or 1 .

However you can create a pseudolog scale using scales::pseudo_log_trans to get 0 included on the axis so all the bars go the same direciton. I'm borrowing from this answer. Compare the two plots below:

library(tidyverse)
library(scales)

# make up data with distribution positive values above and below 1
d <- tibble(grp = LETTERS[1:5],
            val = 10^(-2:2))

# normal plot with true log scale doesn't contain 0
d %>%
  ggplot(aes(x = grp, y = val, fill = grp)) +
  geom_col() +
  ggtitle("On True Log Scale Bars Start at y = 1") +
  scale_y_log10() # or if you prefer: scale_y_continuous(trans = "log10")

# set range of 'linear' portion of pseudolog scale
sigma <- min(d$val)
  
# plot on pseudolog to get all bars to extend to 0
d %>%
  ggplot(aes(x = grp, y = val, fill = grp)) +
  geom_col() +
  ggtitle("On Pseudolog Scale Bars Start at y = 0") +
  scale_y_continuous(
    trans = pseudo_log_trans(base = 10, sigma = sigma),
    breaks = 10^(-2:2)
  )

^{Created on 2021-12-30 by the reprex package (v2.0.1)}