How can I preserve the order I decide in divergent plot

Question

I want to follow this order = genes_order, which I guess is modified by the "stat = identity", overriding it. I don't know how to keep it this way, without the interference of quantitative (if so, because it's not clear) order

The order

genes_order <- c("ABCA1","ABCG1","NR1H2","NR1H3","PPARA",
"PPARD","PPARG","RXRA","RXRB")

df_plot2$gen <- as.factor(df_plot2$gen)
df_plot2 <- as.data.frame(df_plot2)
df_plot2 <- df_plot2[order(df_plot2$gen), ]

The plot: as you can see the order is altered

p1 <- ggplot(data = df_plot2, aes(x = reorder(gen, RQ_gapdh), y = RQ_gapdh, ymin = after_scale(1), fill = Color)) +  geom_bar(stat = "identity", aes(fill=Color), width=.5)+
  labs(x = "Genes", y = 2^-ddCt~ "value",
       title = "Gene expression",
       subtitles = "1 year post-intervention")+
  guides(fill = F) +
  coord_flip()+
  facet_wrap(~grup_int, labeller = labeller(grup_int = c("1" = "Olive oil", "2" = "Nuts", "3" = "Low-fat diet")))

This is my df

df_plot2 <- 
structure(list(gen = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 
3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L, 
8L, 9L, 9L, 9L), levels = c("ABCA1", "ABCG1", "NR1H2", "NR1H3", 
"PPARA", "PPARD", "PPARG", "RXRA", "RXRB"), class = "factor"), 
    grup_int = structure(c(3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L, 
    3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L, 
    3L, 2L, 1L), levels = c("1", "2", "3"), class = "factor"), 
    time = c("3", "3", "3", "3", "3", "3", "3", "3", "3", "3", 
    "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", 
    "3", "3", "3", "3", "3"), RQ_gapdh = c(1.019, 1.218, 1.183, 
    0.926, 1.132, 1.052, 0.936, 1.117, 0.961, 0.987, 1.182, 0.971, 
    1.008, 0.985, 0.951, 0.935, 1.149, 1.058, 0.914, 1.01, 0.952, 
    0.913, 1.134, 1.112, 0.985, 1.074, 1.135), Color = structure(c(2L, 
    2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 
    2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L), levels = c("FALSE", 
    "TRUE"), class = "factor")), row.names = c(8L, 17L, 26L, 
9L, 18L, 27L, 5L, 14L, 23L, 4L, 13L, 22L, 1L, 10L, 19L, 2L, 11L, 
20L, 3L, 12L, 21L, 6L, 15L, 24L, 7L, 16L, 25L), class = "data.frame")

Answer 1

The issue is that you reorder() your gen variable. Drop that and you should be fine. And if you want to reverse the order then could do so by setting limits=rev in scale_x/y_discrete.

Note: I dropped the coord_flip and switched the mapping on x and y instead.

library(ggplot2)

ggplot(data = df_plot2, aes(
  x = RQ_gapdh, y = gen,
  fill = Color
)) +
  geom_col(width = .5) +
  scale_y_discrete(limits = rev) +
  labs(
    y = "Genes", x = 2^-ddCt ~ "value",
    title = "Gene expression",
    subtitles = "1 year post-intervention"
  ) +
  guides(fill = "none") +
  facet_wrap(~grup_int,
    labeller = labeller(
      grup_int = c(
        "1" = "Olive oil",
        "2" = "Nuts",
        "3" = "Low-fat diet"
      )
    )
  )