Missing only one bar in bar-chart

Question

I'm working on a duplicate bar chart using ggplot and I'm almost getting what I want, except for this error I couldn't fix.

The data I'm plotting:

      comp     reg counts
1   C0xC12      up    569
2   C0xC12    down    845
3   C0xC24      up    420
4   C0xC24    down    227
5   C0xT12      up   2904
6   C0xT12    down   2989
7   C0xT24      up   2536
8   C0xT24    down   2309
9  C12xC24      up    314
10 C12xC24    down    138
11 C12xT12      up   3006
12 C12xT12    down   3082
13 C12xT24      up   2795
14 C12xT24    down   2577
15 C24xT12      up   1381
16 C24xT12    down   1901
17 C24xT24      up    482
18 C24xT24    down    862
19 T12xT24      up   1732
20 T12xT24    down   1464
21  C0xC12   uppcw      7
22  C0xC12 downpcw     15
23  C0xC24   uppcw     10
24  C0xC24 downpcw      4
25  C0xT12   uppcw     56
26  C0xT12 downpcw     58
27  C0xT24   uppcw     49
28  C0xT24 downpcw     41
29 C12xC24   uppcw      8
30 C12xC24 downpcw      2
31 C12xT12   uppcw     64
32 C12xT12 downpcw     50
33 C12xT24   uppcw     48
34 C12xT24 downpcw     39
35 C24xT12   uppcw     35
36 C24xT12 downpcw     40
37 C24xT24   uppcw     11
38 C24xT24 downpcw     15
39 T12xT24   uppcw     33
40 T12xT24 downpcw     30

The code I'm running:

teste <- read.table("teste.txt", sep = "\t", header = TRUE)
ggplot(data = teste, 
       mapping = aes(x = comp, fill = reg,
                     y = ifelse(test = reg == "down" | reg == "downpcw", 
                                yes = -counts, no = counts))) +
  geom_bar(stat = "identity") +
  scale_y_continuous(labels = abs, limits = max(teste$counts) * c(-1,1)) +
  geom_text(aes(label=counts), vjust=0.5, color="black", size=3.0, nudge_y = c(-130,130))+
  labs(y = "DEGs", x = "Groups comparisons") + scale_fill_manual(values=c("#98FB98","#FA8072","#00FF00","#FF0000")) +
  scale_x_discrete(limits=c("T12xT24", "C24xT24", "C24xT12", "C12xT24", "C12xT12", "C12xC24", "C0xT24", "C0xT12", "C0xC24","C0xC12")) +
  coord_flip()

That's the plot I'm getting

notice that "C12xT12" biggest bar is not showing, just its size (3082).

I've looked for solutions but found nothing and I can't come up with one alone, so I'm asking if anyone has ever dealt with this issue before.

Answer 1

The problem comes from your scale_y_continuous. You're setting it to the max of the counts column which cuts off the max column as it's exactly at the limit of the plot. If you multiply the max with 1.05 instead of 1, everything should work.
Change the corresponding part of the scale_y_continuous to: limits = max(teste$counts) * c(-1.05,1.05).

Also some best practice colour advice: avoid using red-green combination as ~10% of men are colourblind and cannot tell shades of these colours apart.

Answer 2

The line scale_y_continuous(labels = abs, limits = max(teste$counts) * c(-1,1)) + is "guilty" here, because it limits the axis to exactly 3082. This causes ggplot to clip the bar. Either leave out the limits = max(teste$counts) * c(-1,1) or use something like scale_y_continuous(labels = abs, limits = max(teste$counts) * c(-1.02,1.02)) +