change order of violin plots in ggplot2

Question

Hi there just started to work with violin plots in R and I'm pretty fine with the results but, for some reason, despite attempting various alternatives I cannot change the order of the plots on the x-axis. See below for an example:

Essentially, what I have here is a series of violin plots for eight populations where I show their variants stats; I want them to be ordered as follow: AFR, EUR, MENA, SAS, CEA, SIB, OCE and AME supposedly recapitulating the diminishing total variants found in each group.

This is the code I'm using:

library(dplyr)
library(readxl)
library(tibble)
library(ggplot2)
library(hrbrthemes)
library(introdataviz)

variants_dist <- read_excel("path/to/file.xlsm", 10)
df_var = variants_dist %>% group_by(population_ID) %>% summarise(num=n())

### PLOT THE DATA
variants_dist %>%
  left_join(df_var) %>%
  mutate(pop_count = paste0(population_ID, "\n", "n=", num)) %>%
  ggplot(aes(x=pop_count, y=snps, fill=population_ID)) +
  geom_violin(position="dodge", trim=FALSE) +
  geom_boxplot(width=0.07, color="black", alpha=0.6) +
  scale_fill_manual(values=c(EUR="dodgerblue2", MENA="mediumvioletred", SIB="darkkhaki", CEA="firebrick2", AFR="olivedrab2", OCE="powderblue", SAS="darksalmon", AME="plum2")) +
  #scale_x_discrete(limits = c("AFR", "EUR", "MENA", "SAS", "CEA", "SIB", "OCE", "AME")) +
  theme_bw() +
  theme(
    legend.position="none",
  ) +
  xlab("")

I've followed one of the proposed tutorial to get to this result but, unfortunately, something as basic as changing the order which I normally do with factor specifying the desired sequence for the levels seems to not be working... I commented a line which sets the x-scale as discrete and overlay the theme_bw() option which I found here but I'm not necessarily prone to use.

Any help is much appreciated, I suspect the problem might be the initial left_join(df_var) %>%, if so I still don't know how to get around it. Any help is greatly appreciated, thanks!

dput() output

structure(list(samples = c("abh100 - number of:", "abh107 - number of:", "ALB212 - number of:", "Ale14 - number of:", "Ale20 - number of:", "Ale22 - number of:", "Ale32 - number of:", "altai363p - number of:", "armenia293 - number of:", "Armenian222 - number of:", "AV-21 - number of:", "Ayodo_430C - number of:", "Ayodo_502C - number of:", "Ayodo_81S - number of:", "B11 - number of:", "B17 - number of:", "Bishkek28439 - number of:", "Bishkek28440 - number of:", "Bu16 - number of:", "Bu5 - number of:", "BulgarianB4 - number of:", "BulgarianC1 - number of:", "ch113 - number of:", "CHI-007 - number of:", "CHI-034 - number of:", "DNK05 - number of:", "DNK07 - number of:", "DNK11 - number of:", "Dus16 - number of:", "Dus22 - number of:", "Esk29 - number of:", "Est375 - number of:", "Est400 - number of:", "HG00126 - number of:", "HG00128 - number of:"), population_ID = c("MENA", "MENA", "EUR", "SIB", "SIB", "SIB", "SIB", "SIB", "EUR", "EUR", "EUR", "AFR", "AFR", "AFR", "SAS", "SAS", "SIB", "SIB", "CEA", "CEA", "EUR", "EUR", "EUR", "CEA", "CEA", "AFR", "AFR", "AFR", "OCE", "OCE", "SIB", "EUR", "EUR", "EUR", "EUR"), snps = c(4847876, 4820146, 4875942, 4848405, 4846958, 4893150, 4886498, 4778500, 4868602, 4861225, 5513106, 5726596, 5766508, 5372587, 4974419, 4894272, 4870208, 4913870, 4923787, 4925207, 4840414, 4798908, 4891562, 4953420, 4881495, 5605004, 5703805, 5643221, 4831148, 4829405, 4688483, 4783761, 4778239, 4774887, 4811481)), class = c("tbl_df", "tbl", "data.frame"), row.names = c(NA, -35L))

EDIT for @stefan

variants_dist <- variants_dist %>%
  mutate(population_ID=factor(population_ID, levels=c("AFR", "EUR", "MENA", "SAS", "CEA", "SIB", "OCE", "AME")))

variants_dist %>% arrange(population_ID) -> pop_sort

Then, I changed the x=pop_count to x=forcats::fct_inorder(pop_count)

Is this what you meant in your comment?

Answer 1

This seems to work. Because no levels are supplied to fct, they are computed from the unique values in the order in which they occur, and they've been pre-arranged in the required order.

df_var = variants_dist %>% group_by(population_ID) %>% summarise(num=n())

### PLOT THE DATA
variants_dist %>%
  left_join(df_var) %>%
  arrange(factor(population_ID, levels = c("AFR", "EUR", "MENA", "SAS", "CEA", "SIB", "OCE", "AME"))) |> 
  mutate(pop_count = paste0(population_ID, "\n", "n=", num)) %>%
  mutate(pop_count = fct(pop_count)) %>%
  ggplot(aes(x=pop_count, y=snps, fill=population_ID)) +
  geom_violin(position="dodge", trim=FALSE) +
  geom_boxplot(width=0.07, color="black", alpha=0.6) +
  scale_fill_manual(values=c(EUR="dodgerblue2", MENA="mediumvioletred", SIB="darkkhaki", CEA="firebrick2", AFR="olivedrab2", OCE="powderblue", SAS="darksalmon", AME="plum2")) +
  theme_bw() +
  theme(
    legend.position="none",
  ) +
  xlab("")

^{Created on 2024-03-19 with reprex v2.1.0}