overlaying geom_boxplot() with geom_point
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a11_msp
Apr 27, 2009, 12:16:44 PM4/27/09
to ggplot2
Hi everyone,
I have the following table:
head(res)
ID TF TIME VAL PAR
1 1 X 2 -0.52 1.02
2 1 X 4 0.75 2.23
3 1 Y 2 1.45 1.32
4 1 Y 4 0.84 1.88
5 2 X 2 1.66 1.02
6 2 X 4 3.07 2.23
First, I'm plotting a set of stacked boxplots of VAL for each TF/TIME
combination and this works fine:
p = ggplot(data=res)+
geom_boxplot(aes(x=factor(TF), y=VAL, fill=factor(TIME)))
Now I'm trying to overlay each boxplot with a set of points
corresponding to another parameter, PAR, so I do:
p + geom_point(aes(x=factor(TF),y=MEDIAN, colour=factor(TIME))
Ideally, I would like the X coordinate of the points to coincide with
the centres of the boxplots.
With the default parameters of position to geom_boxplot, setting
fill=factor(TIME) automatically shifts the boxplots so they are
positioned next to each other. The code above obviously does not take
this shift into account and so the X coordinate is the same for both
levels of factor(TIME).
Is there any way to tell geom_point to shift the X coordinate
accordingly?
Actually, perhaps geom_point() isn't even the best way of plotting
this, because (as you may have noticed above) there's actually only a
single value of PAR for each TF/TIME combination - ie, one per
boxplot. What I currently do is just plot loads of PAR points on top
of each other. So if there's a different function suitable for this
purpose, which can better handle the shift in position, this would be
as good.
Many thanks,
Mikhail
--
Mikhail Spivakov, PhD
European Molecular Biology Laboratory
I have the following table:
head(res)
ID TF TIME VAL PAR
1 1 X 2 -0.52 1.02
2 1 X 4 0.75 2.23
3 1 Y 2 1.45 1.32
4 1 Y 4 0.84 1.88
5 2 X 2 1.66 1.02
6 2 X 4 3.07 2.23
First, I'm plotting a set of stacked boxplots of VAL for each TF/TIME
combination and this works fine:
p = ggplot(data=res)+
geom_boxplot(aes(x=factor(TF), y=VAL, fill=factor(TIME)))
Now I'm trying to overlay each boxplot with a set of points
corresponding to another parameter, PAR, so I do:
p + geom_point(aes(x=factor(TF),y=MEDIAN, colour=factor(TIME))
Ideally, I would like the X coordinate of the points to coincide with
the centres of the boxplots.
With the default parameters of position to geom_boxplot, setting
fill=factor(TIME) automatically shifts the boxplots so they are
positioned next to each other. The code above obviously does not take
this shift into account and so the X coordinate is the same for both
levels of factor(TIME).
Is there any way to tell geom_point to shift the X coordinate
accordingly?
Actually, perhaps geom_point() isn't even the best way of plotting
this, because (as you may have noticed above) there's actually only a
single value of PAR for each TF/TIME combination - ie, one per
boxplot. What I currently do is just plot loads of PAR points on top
of each other. So if there's a different function suitable for this
purpose, which can better handle the shift in position, this would be
as good.
Many thanks,
Mikhail
--
Mikhail Spivakov, PhD
European Molecular Biology Laboratory
a11_msp
Apr 27, 2009, 1:20:35 PM4/27/09
to ggplot2
Sorry there was a typo in the code example I gave:
p + geom_point(aes(x=factor(TF),y=MEDIAN, colour=factor(TIME))
should read:
p + geom_point(aes(x=factor(TF),y=PAR, colour=factor(TIME))
p + geom_point(aes(x=factor(TF),y=MEDIAN, colour=factor(TIME))
should read:
p + geom_point(aes(x=factor(TF),y=PAR, colour=factor(TIME))
hadley wickham
Apr 28, 2009, 2:36:07 PM4/28/09
to a11_msp, ggplot2
Hi Mikhail,
Could you also please provide your data in a data that's easy for us
to load into R? The simplest approach is just to paste the output of
dput(res)) (or some sample there of) in to your email.
Hadley
--
http://had.co.nz/
Could you also please provide your data in a data that's easy for us
to load into R? The simplest approach is just to paste the output of
dput(res)) (or some sample there of) in to your email.
Hadley
http://had.co.nz/
Mikhail Spivakov
Apr 28, 2009, 4:31:09 PM4/28/09
to hadley wickham, ggplot2
Hi Hadley,
Here's the output of dput(res):
structure(list(ID = c(6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19,
19, 19, 19, 19, 19, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31,
31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33,
33, 33, 33, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 35,
35, 35, 35, 35, 35, 35, 35, 35, 35, 36, 36, 36, 36, 36, 36, 36,
36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 47, 47, 47,
47, 47, 47, 47, 47, 47, 47), TF = c("X", "X", "Y", "Y", "Z",
"Z", "A", "A", "B", "B", "X", "X", "Y", "Y", "Z", "Z", "A", "A",
"B", "B", "X", "X", "Y", "Y", "Z", "Z", "A", "A", "B", "B", "X",
"X", "Y", "Y", "Z", "Z", "A", "A", "B", "B", "X", "X", "Y", "Y",
"Z", "Z", "A", "A", "B", "B", "X", "X", "Y", "Y", "Z", "Z", "A",
"A", "B", "B", "X", "X", "Y", "Y", "Z", "Z", "A", "A", "B", "B",
"X", "X", "Y", "Y", "Z", "Z", "A", "A", "B", "B", "X", "X", "Y",
"Y", "Z", "Z", "A", "A", "B", "B", "X", "X", "Y", "Y", "Z", "Z",
"A", "A", "B", "B"), TIME = c(2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2,
4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4,
2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2,
4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4,
2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2,
4, 2, 4, 2, 4), VAL = c(-0.52, 0.75, 1.45, 0.84, 1.66, 3.07,
3.53, 4.1, 3.58, 2.5, -0.2, 1.34, 0.58, 1.58, 0.73, 3, 3.84,
4.35, 2.67, 1.75, 1.27, 0.81, 0.28, 0.9, -0.53, 1.95, 3.95, 3.92,
2.95, 1.59, 0.57, 0.86, 1.01, 1.27, 0.38, 0.8, 1.91, 2.43, 2.99,
1.01, 1.52, 1.94, -0.1, 1.03, -0.01, 2.64, 4.19, 3.99, 3.74,
3.14, 0.36, 1.56, 0.26, 0.53, 1.13, 2.4, 4.84, 5.21, 3.4, 0.76,
-0.33, -0.47, 1.2, 1.69, 0.92, 0.7, -0.47, -0.01, 6.48, 3.44,
2.29, 0.58, 1.03, 1.53, 2.23, 0.74, 0.56, 0.2, 7.68, 1.51, 1.95,
1.64, 2.91, 3.14, 2.99, 3.01, 4.04, 3.91, 4.55, 1.74, 2.15, 2.65,
-0.09, 1.8, 1.84, 1.73, 0.99, 1.26, 4.28, 4.1), PAR = c(0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734, 0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734, 0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734, 0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734, 0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734)), .Names = c("ID",
"TF", "TIME", "VAL", "PAR"), row.names = c(NA, 100L), class = "data.frame")
And the code to generate the plot is:
p = ggplot(data=res)+
geom_boxplot(aes(x=factor(TF), y=VAL, fill=factor(TIME)))+
geom_point(aes(x=factor(TF),y=PAR, colour=factor(TIME)))
As I said, what I'm trying to achieve is for the X coordinate of the
points to coincide with the middle of the respective boxplots.
Many thanks,
Mikhail
Here's the output of dput(res):
structure(list(ID = c(6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19,
19, 19, 19, 19, 19, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31,
31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33,
33, 33, 33, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 35,
35, 35, 35, 35, 35, 35, 35, 35, 35, 36, 36, 36, 36, 36, 36, 36,
36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 47, 47, 47,
47, 47, 47, 47, 47, 47, 47), TF = c("X", "X", "Y", "Y", "Z",
"Z", "A", "A", "B", "B", "X", "X", "Y", "Y", "Z", "Z", "A", "A",
"B", "B", "X", "X", "Y", "Y", "Z", "Z", "A", "A", "B", "B", "X",
"X", "Y", "Y", "Z", "Z", "A", "A", "B", "B", "X", "X", "Y", "Y",
"Z", "Z", "A", "A", "B", "B", "X", "X", "Y", "Y", "Z", "Z", "A",
"A", "B", "B", "X", "X", "Y", "Y", "Z", "Z", "A", "A", "B", "B",
"X", "X", "Y", "Y", "Z", "Z", "A", "A", "B", "B", "X", "X", "Y",
"Y", "Z", "Z", "A", "A", "B", "B", "X", "X", "Y", "Y", "Z", "Z",
"A", "A", "B", "B"), TIME = c(2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2,
4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4,
2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2,
4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4,
2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2, 4, 2,
4, 2, 4, 2, 4), VAL = c(-0.52, 0.75, 1.45, 0.84, 1.66, 3.07,
3.53, 4.1, 3.58, 2.5, -0.2, 1.34, 0.58, 1.58, 0.73, 3, 3.84,
4.35, 2.67, 1.75, 1.27, 0.81, 0.28, 0.9, -0.53, 1.95, 3.95, 3.92,
2.95, 1.59, 0.57, 0.86, 1.01, 1.27, 0.38, 0.8, 1.91, 2.43, 2.99,
1.01, 1.52, 1.94, -0.1, 1.03, -0.01, 2.64, 4.19, 3.99, 3.74,
3.14, 0.36, 1.56, 0.26, 0.53, 1.13, 2.4, 4.84, 5.21, 3.4, 0.76,
-0.33, -0.47, 1.2, 1.69, 0.92, 0.7, -0.47, -0.01, 6.48, 3.44,
2.29, 0.58, 1.03, 1.53, 2.23, 0.74, 0.56, 0.2, 7.68, 1.51, 1.95,
1.64, 2.91, 3.14, 2.99, 3.01, 4.04, 3.91, 4.55, 1.74, 2.15, 2.65,
-0.09, 1.8, 1.84, 1.73, 0.99, 1.26, 4.28, 4.1), PAR = c(0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734, 0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734, 0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734, 0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734, 0.349974351871954,
0.314372599616707, 0.366158192067888, 0.286869398822942, 0.367861169367239,
0.347178403222464, 0.355099310185781, 0.324241722657399, 0.0766259660968184,
0.292224064036734, 0.349974351871954, 0.314372599616707, 0.366158192067888,
0.286869398822942, 0.367861169367239, 0.347178403222464, 0.355099310185781,
0.324241722657399, 0.0766259660968184, 0.292224064036734)), .Names = c("ID",
"TF", "TIME", "VAL", "PAR"), row.names = c(NA, 100L), class = "data.frame")
And the code to generate the plot is:
p = ggplot(data=res)+
geom_boxplot(aes(x=factor(TF), y=VAL, fill=factor(TIME)))+
geom_point(aes(x=factor(TF),y=PAR, colour=factor(TIME)))
As I said, what I'm trying to achieve is for the X coordinate of the
points to coincide with the middle of the respective boxplots.
Many thanks,
Mikhail
hadley wickham
Apr 28, 2009, 4:46:51 PM4/28/09
to Mikhail Spivakov, ggplot2
> And the code to generate the plot is:
>
> p = ggplot(data=res)+
> geom_boxplot(aes(x=factor(TF), y=VAL, fill=factor(TIME)))+
> geom_point(aes(x=factor(TF),y=PAR, colour=factor(TIME)))
>
> As I said, what I'm trying to achieve is for the X coordinate of the
> points to coincide with the middle of the respective boxplots.
>
> p = ggplot(data=res)+
> geom_boxplot(aes(x=factor(TF), y=VAL, fill=factor(TIME)))+
> geom_point(aes(x=factor(TF),y=PAR, colour=factor(TIME)))
>
> As I said, what I'm trying to achieve is for the X coordinate of the
> points to coincide with the middle of the respective boxplots.
Well the easiest way is to switch to using facetting:
ggplot(res, aes(factor(TIME))) +
geom_boxplot(aes(y = VAL, fill = factor(TIME))) +
geom_point(aes(y = PAR, colour = factor(TIME))) +
facet_wrap(~ TF, nrow = 1)
Hadley
Mikhail Spivakov
Apr 28, 2009, 4:59:18 PM4/28/09
to hadley wickham, ggplot2
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