Specify tick marks on y-axis ggplot2

Question

Here is what my test data looks like (this is fake data):

   Var1 Var2     value
1     A   -7 0.7239130
2     C   -7 0.8326087
3     G   -7 0.7891304
4     U   -7 0.8543478
5     A   -6 0.7673913
6     C   -6 0.8326087
7     G   -6 0.7673913
8     U   -6 0.8326087
9     A   -5 0.8543478
10    C   -5 0.7239130
11    G   -5 0.8760870
12    U   -5 0.7456522
13    A   -4 0.8108696
14    C   -4 0.7456522
15    G   -4 0.8108696
16    U   -4 0.8326087
17    A   -3 0.8543478
18    C   -3 0.7456522
19    G   -3 0.8108696
20    U   -3 0.7891304
21    A   -2 0.7456522
22    C   -2 0.8543478
23    G   -2 0.8326087
24    U   -2 0.7673913
25    A   -1 0.8760870
26    C   -1 0.8326087
27    G   -1 0.5934783
28    U   -1 0.8978261
29    A    0        NA
30    C    0        NA
31    G    0        NA
32    U    0        NA
33    A    1 0.6804348
34    C    1 0.9847826
35    G    1 0.8978261
36    U    1 0.6369565
37    A    2 0.9195652
38    C    2 0.7891304
39    G    2 0.7891304
40    U    2 0.7021739
41    A    3 0.7891304
42    C    3 0.7239130
43    G    3 0.8108696
44    U    3 0.8760870
45    A    4 0.7021739
46    C    4 0.8326087
47    G    4 0.7673913
48    U    4 0.8978261
49    A    5 0.6804348
50    C    5 0.8543478
51    G    5 0.8108696
52    U    5 0.8543478
53    A    6 0.7456522
54    C    6 0.7456522
55    G    6 0.7891304
56    U    6 0.9195652
57    A    7 0.8326087
58    C    7 0.8326087
59    G    7 0.7456522
60    U    7 0.7891304

Here is my code for ggplot2:

  ggplot(data=test, aes(x=Var2, y=value, fill=Var1))+
  geom_bar(stat="identity", position=position_dodge(), colour="black")+
  scale_fill_manual(values=c("grey80","grey20","blue","lightblue"))+
  theme_bw()+
  ylim(0, 1)+
  ggtitle("example")+
  theme(legend.direction="horizontal", legend.key.size=unit(18,"points"), legend.justification=c(1,1), legend.position=c(1,0.25), legend.title=element_blank())+
  scale_x_continuous(limits = c(-7.5,7.5), breaks = round(seq(-7,7)),1)+
  xlab("position")+ylab("arbitrary value")+
  geom_hline(yintercept = 0.5, linetype=3)

Here is the output:

I would like to specify the ticks on the y-axis so that it is labeled 0, 0.1, 0.2, 0.3... I tried using scale_y_continuous but it erased the entire y-labels. Most tutorials solely focus on the x-axis. How am I supposed to do this?

Solution

You have to remove the ylim function and input the scale_y_continuous one

ggplot(data=test, aes(x=Var2, y=value, fill=Var1))+
   geom_bar(stat="identity", position=position_dodge(), colour="black")+
   scale_fill_manual(values=c("grey80","grey20","blue","lightblue"))+
   theme_bw()+
   scale_y_continuous(breaks = seq(0, 1, .1), limits = c(0, 1)) +
   ggtitle("example")+
   #theme(legend.direction="horizontal", 
   #      legend.key.size=unit(18,"points"),
   #      legend.justification=c(1,1), 
   #      legend.position=c(1,0.25), 
   #      legend.title=element_blank()) +
   scale_x_continuous(limits = c(-7.5,7.5), breaks = round(seq(-7,7)),1)+
   xlab("position")+ylab("arbitrary value")+
   geom_hline(yintercept = 0.5, linetype=3)

Comments

[joran]

I'm not sure exactly what your problem is. Adding scale_y_continuous(breaks = seq(0,1,by = 0.1)) to your graph works just fine for me (and that's no different that what you did for the x axis).

[biohazard]

I did try that at first but I don't know why it didn't work. Then I tried maloneypatr's answer below and it gave me super long values so I used round() to counter that and it's working now. I may have made a mistake but I don't think my question is useless for the community, since I couldn't find a question describing y-ticks settings.

[joran]

Not using both ylim and scale_y_continuous may be cleaner, but it is not necessary: adding scale_y_continuous works just fine even if you leave ylim in (although you do get a warning, of course).

[biohazard]

Is there a reason why you commented out theme()+?

[biohazard]

When I implement your solution with scale_y_continuous(breaks = seq(-0.3, 0.3, .1), limits = c(-0.35, 0.35)) +, I get super long values on the y-axis such as 3.000000e-1, 2.000000e-1, 1.000000e-1, 5.551115e-17...

[biohazard]

Oh, nevermind, it works perfectly with round(seq(-0.3,0.3,.1),2)! Maybe you can add it to your solution :D

[Elisabeth]

Is there a way to add a custom y tick mark at one specific point (to call out a special y value on the graph)? Thank you