How to insert blank space on x-axis in boxplot using ggplot /R?

Question

I have My Data stored in p, which can be found below.

I have four specific categories for a group of tumor patients. Three of the groups correspond to the tumor stage and is stored as p$WHO.Grade=1,2,3. The last group is All tumor patients combined.

I am producing a specific plot consisting of multiple boxplots demonstrating the distribution of a continuous covariate (p$ki67pro) in the four groups described as above and in relation to the event of recurrence (p$recurrence==0 for no and p$recurrence==1 for yes).

As it turns out, there are no events for p$WHO.Grade==3, which means that I want my blot to look exactly like this (manipulated in photoshop):

However, I get the picture below when I use the following script:

library(ggplot2)
library(dplyr)    
p %>%
      bind_rows(p %>% mutate(WHO.Grade = 4)) %>%
      mutate(WHO.Grade = factor(WHO.Grade),
             recurrence = factor(recurrence)) %>%
      ggplot(aes(WHO.Grade, ki67pro, 
                 fill = recurrence, colour = recurrence)) +
      geom_boxplot(outlier.alpha = 0, 
                   position = position_dodge(width = 0.78, preserve = "single")) +
      geom_point(size = 3, shape = 21, 
                 position = position_jitterdodge()) +
      scale_x_discrete(name = "", 
                       label = c("WHO-I","WHO-II","WHO-III","All")) +
      scale_y_continuous(name = "x", breaks=seq(0,30,5), limits=c(0,30)) +
      scale_fill_manual(values = c("#edf1f9", "#fcebeb"), name = "",
                        labels = c("", "")) +
      scale_colour_manual(values = c("#1C73C2", "red"), name = "",
                          labels = c("","")) + 
      theme(legend.position="none",
            panel.background = element_blank(),
            axis.line = element_line(colour = "black"))

It seems like p$WHO.Grade==All automatically is inserted at the p$WHO.Grade==3 space, which should be leaved blank.

Therefore, my question is: how can I graphically insert a blank space at p$WHO.Grade==3 given my script above?

p <- structure(list(WHO.Grade = c(1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 
                                  1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 
                                  1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
                                  1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 
                                  1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 
                                  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
                                  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 
                                  1L, 1L, 1L, 1L, 1L, 1L), ki67pro = c(1L, 12L, 3L, 3L, 5L, 3L, 
                                                                       25L, 7L, 4L, 5L, 12L, 3L, 15L, 4L, 5L, 7L, 8L, 3L, 12L, 10L, 
                                                                       4L, 10L, 7L, 3L, 2L, 3L, 7L, 4L, 7L, 10L, 4L, 5L, 5L, 3L, 5L, 
                                                                       2L, 5L, 3L, 3L, 3L, 4L, 4L, 3L, 2L, 5L, 1L, 5L, 2L, 3L, 1L, 2L, 
                                                                       3L, 3L, 5L, 4L, 20L, 5L, 0L, 4L, 3L, 0L, 3L, 4L, 1L, 2L, 20L, 
                                                                       2L, 3L, 5L, 4L, 8L, 1L, 4L, 5L, 4L, 3L, 6L, 12L, 3L, 4L, 4L, 
                                                                       2L, 5L, 3L, 3L, 3L, 2L, 5L, 4L, 2L, 3L, 4L, 3L, 3L, 2L, 2L, 4L, 
                                                                       7L, 4L, 3L, 4L, 2L, 3L, 6L, 2L, 3L, 10L, 5L, 10L, 3L, 10L, 3L, 
                                                                       4L, 5L, 2L, 4L, 3L, 4L, 4L, 4L, 5L, 3L, 12L, 5L, 4L, 3L, 2L, 
                                                                       4L, 3L, 4L, 2L, 1L, 6L, 1L, 4L, 12L, 3L, 4L, 3L, 2L, 6L, 5L, 
                                                                       4L, 3L, 4L, 4L, 4L, 3L, 5L, 4L, 5L, 4L, 1L, 3L, 3L, 4L, 0L, 3L
                                  ), recurrence = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 
                                                    0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 
                                                    1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
                                                    1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 
                                                    1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 
                                                    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
                                                    0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 
                                                    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
                                                    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
                                                    0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 
                                                    0L, 0L, 0L)), class = "data.frame", row.names = c(1L, 2L, 3L, 
                                                                                                      9L, 10L, 11L, 13L, 14L, 15L, 16L, 18L, 19L, 20L, 21L, 22L, 23L, 
                                                                                                      24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 
                                                                                                      37L, 38L, 39L, 40L, 41L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 
                                                                                                      52L, 53L, 54L, 55L, 57L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 
                                                                                                      67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 
                                                                                                      80L, 81L, 82L, 83L, 84L, 85L, 87L, 89L, 90L, 91L, 92L, 93L, 94L, 
                                                                                                      96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 
                                                                                                      107L, 109L, 110L, 111L, 112L, 113L, 114L, 115L, 116L, 117L, 118L, 
                                                                                                      119L, 120L, 121L, 123L, 124L, 125L, 126L, 127L, 128L, 130L, 131L, 
                                                                                                      132L, 133L, 134L, 135L, 136L, 137L, 138L, 139L, 140L, 141L, 142L, 
                                                                                                      143L, 144L, 145L, 146L, 147L, 148L, 149L, 150L, 151L, 152L, 153L, 
                                                                                                      154L, 155L, 156L, 157L, 158L, 159L, 160L, 161L, 162L, 163L, 164L, 
                                                                                                      165L, 166L, 167L, 168L, 169L, 170L, 171L, 172L, 173L, 174L, 175L
                                                    ))

Cole · Accepted Answer · 2019-09-15 11:24:12Z

The simplest way is to adjust your WHO.Grade factor to include all 4 levels - c("WHO-I","WHO-II","WHO-III","All")```. Here's the first adjustment on line 3:

p %>%
  bind_rows(p %>% mutate(WHO.Grade = 4)) %>%
  mutate(WHO.Grade = factor(WHO.Grade, levels = 1:4, labels = c("WHO-I","WHO-II","WHO-III","All")),
         recurrence = factor(recurrence))

Now that we've named our factors, we can modify the scale_x_discrete() call to remove the label and add drop = FALSE:

  scale_x_discrete(name = "",
                   # label = c("WHO-I","WHO-II","WHO-III","All"),
                   drop = FALSE)

Putting everything together we get:

p %>%
  bind_rows(p %>% mutate(WHO.Grade = 4)) %>% as_tibble()%>%
  mutate(WHO.Grade = factor(WHO.Grade, levels = 1:4, labels = c("WHO-I","WHO-II","WHO-III","All")),
         recurrence = factor(recurrence))%>%
  ggplot(aes(WHO.Grade, ki67pro, 
             fill = recurrence, colour = recurrence)) +
  geom_boxplot(outlier.alpha = 0, 
               position = position_dodge(width = 0.78, preserve = "single")) +
  geom_point(size = 3, shape = 21,
             position = position_jitterdodge()) +
  scale_x_discrete(name = "",
                   # label = c("WHO-I","WHO-II","WHO-III","All"),
                   drop = FALSE) +
  scale_y_continuous(name = "x", breaks=seq(0,30,5), limits=c(0,30)) +
  scale_fill_manual(values = c("#edf1f9", "#fcebeb"), name = "",
                    labels = c("", "")) +
  scale_colour_manual(values = c("#1C73C2", "red"), name = "",
                      labels = c("","")) + 
  theme(legend.position="none",
        panel.background = element_blank(),
        axis.line = element_line(colour = "black"))

David · Accepted Answer · 2019-09-15 18:46:32Z

I could not reach to the result you want as appeared in the Photoshop image, but you could gain the following image:

Which it is what you want, but all the entries of "WHO-III" are zeros

The code that generates it is:

library(ggplot2)
library(dplyr)  

p= p %>%
  bind_rows(p %>% mutate(WHO.Grade = 3)) %>%
  bind_rows(p %>% mutate(WHO.Grade = 4))
p[p$WHO.Grade == 3, 2] = 0

p %>%  
  mutate(WHO.Grade = factor(WHO.Grade),
         recurrence = factor(recurrence)) %>%
  ggplot(aes(WHO.Grade, ki67pro, 
             fill = recurrence, colour = recurrence)) +
  geom_boxplot(outlier.alpha = 0, 
               position = position_dodge(width = 0.78, preserve = "single")) +
  geom_point(size = 3, shape = 21, 
             position = position_jitterdodge()) +
  scale_x_discrete(name = "", 
                   label = c("WHO-I","WHO-II","WHO-III","All"), drop = FALSE) +
  scale_y_continuous(name = "x", breaks=seq(0,30,5), limits=c(0,30)) +
  scale_fill_manual(values = c("#edf1f9", "#fcebeb"), name = "",
                    labels = c("", "")) +
  scale_colour_manual(values = c("#1C73C2", "red"), name = "",
                      labels = c("","")) + 
  theme(legend.position="none",
        panel.background = element_blank(),
        axis.line = element_line(colour = "black"))

Hope this helps

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