Scales and space in faceting
Roberto Osorio
"For facet_grid there is an additional parameter called space, which
takes
values "free" or "fixed". When the space can vary freely, each column
(or
row) will have width (or height) proportional to the range of the
scale for that
column (or row)."
I'm getting unpredictable behavior when using scales="free_y",
space="free". Take the following example:
da <- data.frame(
x=rep(1:5, 2),
y=c(1+(0:4), 1+(0:4)/10),
z=rep(1:2, each=5))
da
# x y z
#1 1 1.0 1
#2 2 2.0 1
#3 3 3.0 1
#4 4 4.0 1
#5 5 5.0 1
#6 1 1.0 2
#7 2 1.1 2
#8 3 1.2 2
#9 4 1.3 2
#10 5 1.4 2
qplot(x, y, data=da, group=z, geom="line") +
# scale_y_log10() +
facet_grid(z~., scales="free_y", space="free")
If the facet heights were proportional to their row ranges, the ratio
of the top to bottom facet heights (i.e., z=1 to z=2), should be (5-1)/
(1.4-1) = 4/0.4 = 10. The observed ratio in the resulting plot is
actually a lot smaller than that.
If you uncomment the log10 option, this problem looks worse: the two
heights now look the same! Instead, the heights ratio should be
log10(5)/log10(1.4) (since log10(1) = 0), i.e., 4.78.
Comments? I'm using R 2.9.1 and ggplot2 0.8.3.
Roberto
hadley wickham
This looks like a bug. Thanks for the clear reproducible example -
I'll add it to my to do list and take a look at it as soon as I get a
chance.
Regards,
Hadley
http://had.co.nz/
Quince Gibson
Just wondering has the bug in spacing when using faceting been fixed
yet?
The following is giving me a fixed x-axis but a lot of space as
chromosomes get higher.
p <- qplot(POS, -log10(SNP_TSCORE_PVAL), colour=CHR2, data = tdata
[tdata$CHR>0,]) + facet_grid(. ~ CHR2, scales="fixed", space="free")
print(p)
Thanks,
Quince.
Hadley Wickham
it's the same problem or not.
Hadley
Sent from my iPhone
Quince Gibson
"hopefully" reproducible example. I would like to create a "manhattan
plot" for Genome-wide association studies using faceting and taking
advantage of the 'space="free"' option when using qplot. POS is base
pair position and needs to be on a fixed x scale so that the distance
between points is important (how far up down the chromosome a
particular point is. Chromosome 1 is the largest and has, for
simplification Positions 0:100. Chr 3 has position 0:40, Chr4 has
positions 0:10.
I expect space=free to break the faceted graphs at their upper postion
limit. This is not happening. Both X and Y scales must be fixed for
publication purpuse
> df <- data.frame(
CHR=rep(1:6,each=3),
POS=c(0,10,20,10,20,30,10,15,20,0,5,10,30,31,32,41,40,42),
SCORE=rep(1:3,6))
> df
CHR POS SCORE
1 1 0 1
2 1 10 2
3 1 20 3
4 2 10 1
5 2 20 2
6 2 30 3
7 3 10 1
8 3 15 2
9 3 20 3
10 4 0 1
11 4 5 2
12 4 10 3
13 5 30 1
14 5 31 2
15 5 32 3
16 6 41 1
17 6 40 2
18 6 42 3
> p <- qplot(POS,SCORE,data=df) + facet_grid(. ~ CHR, scales="fixed", space="free")
> print(p)
Hope this helps,
Quince
On Oct 2, 9:15 pm, Hadley Wickham <h.wick...@gmail.com> wrote:
> Could you please send a reproducible example? It's hard to know if
> it's the same problem or not.
>
> Hadley
>
> Sent from my iPhone
>
hadley wickham
>
> Sorry about that, I was referring to the previous example. Here is a
> "hopefully" reproducible example. I would like to create a "manhattan
> plot" for Genome-wide association studies using faceting and taking
> advantage of the 'space="free"' option when using qplot. POS is base
> pair position and needs to be on a fixed x scale so that the distance
> between points is important (how far up down the chromosome a
> particular point is. Chromosome 1 is the largest and has, for
> simplification Positions 0:100. Chr 3 has position 0:40, Chr4 has
> positions 0:10.
>
> I expect space=free to break the faceted graphs at their upper postion
> limit. This is not happening. Both X and Y scales must be fixed for
> publication purpuse
space = "free" if only meaningful if scales = "free", because when
scales = "fixed" all the scales are the same!
Hadley