CODEWITHSUNDEEP
rggplot2
S Front
S Front

Reputation: 353

Reduce range ggplot y-axis without reducing range of shown data

I would like to restrict the end of the y-axis without restricting the range of the shown data in this plot on the y-axis from 0 to 32. Specifically, the axis should not be shown for higher values but the significance comparison should be included and the part in red should not be shown.

library(ggpubr)
data("ToothGrowth")
head(ToothGrowth)

# Visualize: Specify the comparisons you want
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
ggboxplot(ToothGrowth, x = "dose", y = "len",
      color = "dose", palette = "jco")+ 
  stat_compare_means(comparisons = my_comparisons)+ # Add pairwise comparisons p-value
  stat_compare_means(label.y = 50)     # Add global p-value

example Plot

Upvotes: 3

Views: 593

Answers (3)

teunbrand
teunbrand

Reputation: 38063

You can try guide_axis_truncated() from the ggh4x package. Disclaimer: I'm the author of ggh4x.

library(ggpubr)
#> Warning: package 'ggpubr' was built under R version 4.1.1
#> Loading required package: ggplot2
data("ToothGrowth")
library(ggh4x)

# Visualize: Specify the comparisons you want
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
ggboxplot(ToothGrowth, x = "dose", y = "len",
          color = "dose", palette = "jco")+ 
  stat_compare_means(comparisons = my_comparisons)+ # Add pairwise comparisons p-value
  stat_compare_means(label.y = 50) +
  scale_y_continuous(
    breaks = function(x) {
      x <- scales::extended_breaks()(x)
      x[x < 32]
    },
    guide = guide_axis_truncated(trunc_lower = -Inf, trunc_upper = 32)
  )
#> Warning in wilcox.test.default(c(4.2, 11.5, 7.3, 5.8, 6.4, 10, 11.2, 11.2, :
#> cannot compute exact p-value with ties
#> Warning in wilcox.test.default(c(4.2, 11.5, 7.3, 5.8, 6.4, 10, 11.2, 11.2, :
#> cannot compute exact p-value with ties
#> Warning in wilcox.test.default(c(16.5, 16.5, 15.2, 17.3, 22.5, 17.3, 13.6, :
#> cannot compute exact p-value with ties

Created on 2021-09-24 by the reprex package (v2.0.1)

Upvotes: 3

nucleaR
nucleaR

Reputation: 325

You may try below solution. It limits the y-axis to 35, then tells ggplot to not 'clip' the rest of the data, and to show the annotations that are outside the range of c(0,35), we expand the margins of the plot. Then re-position the legend to your needs. Modify according to your needs:

library(ggpubr)
data("ToothGrowth")
head(ToothGrowth)

# Visualize: Specify the comparisons you want
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
ggboxplot(ToothGrowth, x = "dose", y = "len",
          color = "dose", palette = "jco")+ 
  stat_compare_means(comparisons = my_comparisons)+ # Add pairwise comparisons p-value
  stat_compare_means(label.y = 50) +
  coord_cartesian(clip = "off", ylim = c(0, 35)) +
  theme(plot.margin = unit(c(8,0,0,0), "cm"),
        legend.position = c(.5,1.5),
        legend.direction = "horizontal")

Preview plot

Upvotes: 3

Lucas
Lucas

Reputation: 389

Well, I tried. And it's not perfect - but it is a start ;)

library(ggpubr)
data("ToothGrowth")
head(ToothGrowth)

# Visualize: Specify the comparisons you want
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
ggboxplot(ToothGrowth, x = "dose", y = "len",
          color = "dose", palette = "jco")+ 
  scale_y_continuous(breaks = c(10,20,30), limits = c(0,50)) +
  theme(axis.line.y = element_line(size = 1, colour = "white"))+
  stat_compare_means(comparisons = my_comparisons)+ # Add pairwise comparisons p-value
  stat_compare_means(label.y = 50, label.x = 0.3)+     # Add global p-value
  geom_rect(aes(xmin=0,xmax=0.02,ymin=0,ymax=30), size=0, fill="black")

enter image description here

Upvotes: 2

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