Nathan Miller
2011-Sep-07 21:48 UTC
[R] ggplot2-Issue placing error bars behind data points
Hi all,
This seems like a basic problem, but no amount of playing with the code has
solved it. I have a time-series data set like that shown below (only longer)
and am seeking to plot the data with filled, circular points and error bars.
I would like the error bars to be behind the points otherwise they tend to
obscure the points (especially when I have a lot of points in the actual
data set). Despite providing a fill colour for the points and using shapes
that utilize fill colours, the error bars are always placed on top of the
points. Can anyone see the error I am making? I simply want to move the
error bars so they are behind the data points.
Thanks for your help. I assume its simple...or else its a bug.
Nate
Time SAP Temp SAPSE
0.00 1.000000 25 0.000000
0.25 1.040000 25 0.041200
0.50 1.040000 25 0.093500
0.75 1.060000 25 0.081800
1.00 1.040000 25 0.131000
1.25 1.220000 25 0.144000
1.50 1.010000 25 0.071200
0.00 1.000000 15 0.000000
0.25 1.010000 15 0.015600
0.50 1.010000 15 0.033700
0.75 1.060000 15 0.048100
1.00 1.010000 15 0.016800
1.25 0.977000 15 0.004860
1.50 0.959000 15 0.015500
0.00 1.000000 8 0.000000
0.25 1.010000 8 0.004620
0.50 1.060000 8 0.049100
0.75 0.921000 8 0.032900
1.00 0.951000 8 0.030400
1.25 0.904000 8 0.047100
1.50 0.911000 8 0.072200
limits<-aes(ymax=NerveSurv$SAP+NerveSurv$SAPSE,ymin=NerveSurv$SAP-NerveSurv$SAPSE)
p<-ggplot(data=NerveSurv,aes(x=Time,y=SAP))
p+geom_point(aes(colour=factor(Temp), shape=factor(Temp),
fill=factor(Temp)), size=4)
+geom_errorbar(limits,width=0.2)
+xlab("Time (min)")
+xlim(c(0,50))
+ylab("Normalized Spontaneous Action Potential Rate")
+ylim(c(0,1.6))
+scale_shape_manual("Acclimation Temperature",breaks=c(8,18,25),
labels=c("25 ºC", "18 ºC", "8
ºC"),values=c(21,21,21))
+scale_fill_manual("Acclimation Temperature",breaks=c(8,18,25),
labels=c("25
ºC", "18 ºC", "8
ºC"),values=c(colours()[c(173,253,218)]))
+scale_colour_manual("Acclimation Temperature",breaks=c(8,18,25),
labels=c("25 ºC", "18 ºC", "8 ºC"),
values=c(colours()[c(173,173,173)]))
[[alternative HTML version deleted]]
Jeff Newmiller
2011-Sep-07 21:52 UTC
[R] ggplot2-Issue placing error bars behind data points
Add geom_errorbar() before adding geom_point() ?
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Sent from my phone. Please excuse my brevity.
Nathan Miller <natemiller77@gmail.com> wrote:
Hi all,
This seems like a basic problem, but no amount of playing with the code has
solved it. I have a time-series data set like that shown below (only longer)
and am seeking to plot the data with filled, circular points and error bars.
I would like the error bars to be behind the points otherwise they tend to
obscure the points (especially when I have a lot of points in the actual
data set). Despite providing a fill colour for the points and using shapes
that utilize fill colours, the error bars are always placed on top of the
points. Can anyone see the error I am making? I simply want to move the
error bars so they are behind the data points.
Thanks for your help. I assume its simple...or else its a bug.
Nate
Time SAP Temp SAPSE
0.00 1.000000 25 0.000000
0.25 1.040000 25 0.041200
0.50 1.040000 25 0.093500
0.75 1.060000 25 0.081800
1.00 1.040000 25 0.131000
1.25 1.220000 25 0.144000
1.50 1.010000 25 0.071200
0.00 1.000000 15 0.000000
0.25 1.010000 15 0.015600
0.50 1.010000 15 0.033700
0.75 1.060000 15 0.048100
1.00 1.010000 15 0.016800
1.25 0.977000 15 0.004860
1.50 0.959000 15 0.015500
0.00 1.000000 8 0.000000
0.25 1.010000 8 0.004620
0.50 1.060000 8 0.049100
0.75 0.921000 8 0.032900
1.00 0.951000 8 0.030400
1.25 0.904000 8 0.047100
1.50 0.911000 8 0.072200
limits<-aes(ymax=NerveSurv$SAP+NerveSurv$SAPSE,ymin=NerveSurv$SAP-NerveSurv$SAPSE)
p<-ggplot(data=NerveSurv,aes(x=Time,y=SAP))
p+geom_point(aes(colour=factor(Temp), shape=factor(Temp),
fill=factor(Temp)), size=4)
+geom_errorbar(limits,width=0.2)
+xlab("Time (min)")
+xlim(c(0,50))
+ylab("Normalized Spontaneous Action Potential Rate")
+ylim(c(0,1.6))
+scale_shape_manual("Acclimation Temperature",breaks=c(8,18,25),
labels=c("25 �C", "18 �C", "8
�C"),values=c(21,21,21))
+scale_fill_manual("Acclimation Temperature",breaks=c(8,18,25),
labels=c("25
�C", "18 �C", "8
�C"),values=c(colours()[c(173,253,218)]))
+scale_colour_manual("Acclimation Temperature",breaks=c(8,18,25),
labels=c("25 �C", "18 �C", "8 �C"),
values=c(colours()[c(173,173,173)]))
[[alternative HTML version deleted]]
_____________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
Dennis Murphy
2011-Sep-07 22:33 UTC
[R] ggplot2-Issue placing error bars behind data points
Hi:
For your test data, try this:
# Result of dput(NerveSurv)
NerveSurv <- structure(list(Time = c(0, 0.25, 0.5, 0.75, 1, 1.25, 1.5, 0,
0.25, 0.5, 0.75, 1, 1.25, 1.5, 0, 0.25, 0.5, 0.75, 1, 1.25, 1.5
), SAP = c(1, 1.04, 1.04, 1.06, 1.04, 1.22, 1.01, 1, 1.01, 1.01,
1.06, 1.01, 0.977, 0.959, 1, 1.01, 1.06, 0.921, 0.951, 0.904,
0.911), Temp = c(25L, 25L, 25L, 25L, 25L, 25L, 25L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 8L, 8L, 8L, 8L, 8L, 8L, 8L), SAPSE = c(0,
0.0412, 0.0935, 0.0818, 0.131, 0.144, 0.0712, 0, 0.0156, 0.0337,
0.0481, 0.0168, 0.00486, 0.0155, 0, 0.00462, 0.0491, 0.0329,
0.0304, 0.0471, 0.0722)), .Names = c("Time", "SAP",
"Temp", "SAPSE"
), class = "data.frame", row.names = c(NA, -21L))
limits<-aes(ymax = NerveSurv$SAP + NerveSurv$SAPSE,
ymin = NerveSurv$SAP - NerveSurv$SAPSE)
# library('ggplot2')
p <- ggplot(data=NerveSurv,aes(x=Time,y=SAP))
p + geom_errorbar(limits,width=0.2) +
geom_point(aes(fill=factor(Temp)), colour = colors()[173],
shape = 21, size=4) +
xlab("Time (min)") +
xlim(c(0, 2)) +
ylab("Normalized Spontaneous Action Potential Rate") +
ylim(c(0,1.6)) +
scale_fill_manual("Acclimation\nTemperature", breaks=c(8,18,25),
labels=c("25?C", "18 ?C", "8
?C"),
values=c(colours()[c(173,253,218)]))
Notice the following in the above code:
(1) As Jeff Newmiller pointed out, put geom_errorbar() before geom_point().
(2) If you are going to be using the same value of a plot aesthetic, you
*set* it outside aes() rather than *map* it inside aes().
See the revised code for geom_point(). The idea is that if a
variable is assigned
to a plot aesthetic (e.g., color, fill, shape), then it needs to
be mapped inside
aes(); if an aesthetic is set to a specific value, it is set outside aes().
(3) Your test data had an effective x-range of 0 - 1.5 rather than 0 - 50, so
I shrunk xlim() for readability.
(4) You can use \n inside of a character string as a carriage return. See
the legend title for scale_fill_manual().
(5) Style note: you want the layer addition operator + to be at the end of a
line, not at the beginning. Copy and paste this code verbatim to
see what I mean:
p + geom_errorbar(limits,width=0.2)
+ geom_point(aes(fill=factor(Temp)), colour = colors()[173],
shape = 21, size=4)
This happens because the first line is syntactically complete.
HTH,
Dennis
On Wed, Sep 7, 2011 at 2:48 PM, Nathan Miller <natemiller77 at gmail.com>
wrote:> Hi all,
>
> This seems like a basic problem, but no amount of playing with the code has
> solved it. I have a time-series data set like that shown below (only
longer)
> and am seeking to plot the data with filled, circular points and error
bars.
> I would like the error bars to be behind the points otherwise they tend to
> obscure the points (especially when I have a lot of points in the actual
> data set). Despite providing a fill colour for the points and using shapes
> that utilize fill colours, the error bars are always placed on top of the
> points. Can anyone see the error I am making? I simply want to move the
> error bars so they are behind the data points.
>
> Thanks for your help. I assume its simple...or else its a bug.
>
> Nate
>
>
> ?Time ? ? ?SAP Temp ? ?SAPSE
> ?0.00 1.000000 ? 25 ? ? 0.000000
> ?0.25 1.040000 ? 25 ? ? 0.041200
> 0.50 1.040000 ? 25 ? ? ?0.093500
> 0.75 1.060000 ? 25 ? ? 0.081800
> 1.00 1.040000 ? 25 ? ? 0.131000
> 1.25 1.220000 ? 25 ? ? 0.144000
> 1.50 1.010000 ? 25 ? ? 0.071200
> 0.00 1.000000 ? 15 ? ? 0.000000
> 0.25 1.010000 ? 15 ? ? 0.015600
> ?0.50 1.010000 ? 15 ? ?0.033700
> 0.75 1.060000 ? 15 ? ?0.048100
> 1.00 1.010000 ? 15 ? ?0.016800
> 1.25 0.977000 ? 15 ? ?0.004860
> 1.50 0.959000 ? 15 ? ?0.015500
> 0.00 1.000000 ? ?8 ? ? 0.000000
> 0.25 1.010000 ? ?8 ? ? 0.004620
> 0.50 1.060000 ? ?8 ? ? 0.049100
> 0.75 0.921000 ? ?8 ? ? 0.032900
> 1.00 0.951000 ? ?8 ? ? 0.030400
> 1.25 0.904000 8 ? ? 0.047100
> 1.50 0.911000 8 ? ? 0.072200
>
>
limits<-aes(ymax=NerveSurv$SAP+NerveSurv$SAPSE,ymin=NerveSurv$SAP-NerveSurv$SAPSE)
>
> p<-ggplot(data=NerveSurv,aes(x=Time,y=SAP))
>
> p+geom_point(aes(colour=factor(Temp), shape=factor(Temp),
> fill=factor(Temp)), size=4)
> +geom_errorbar(limits,width=0.2)
> +xlab("Time (min)")
> +xlim(c(0,50))
> +ylab("Normalized Spontaneous Action Potential Rate")
> +ylim(c(0,1.6))
> +scale_shape_manual("Acclimation Temperature",breaks=c(8,18,25),
> labels=c("25 ?C", "18 ?C", "8
?C"),values=c(21,21,21))
> +scale_fill_manual("Acclimation Temperature",breaks=c(8,18,25),
labels=c("25
> ?C", "18 ?C", "8
?C"),values=c(colours()[c(173,253,218)]))
> +scale_colour_manual("Acclimation Temperature",breaks=c(8,18,25),
> labels=c("25 ?C", "18 ?C", "8 ?C"),
values=c(colours()[c(173,173,173)]))
>
> ? ? ? ?[[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>