Dear R-list I'm working with with geom_errorbar; specifically I'm trying to reproduce the example Hadley Wickham have on http://had.co.nz/ggplot2/geom_errorbar.html (all in the button of the page) where he makes an nice plot with errorbars and then draw lines between the points. What confuses me is the 'limits' he defines for the errorbars from the se variable. First he creates a dataset, df <- data.frame( trt = factor(c(1, 1, 2, 2)), resp = c(1, 5, 3, 4), group = factor(c(1, 2, 1, 2)), se = c(0.1, 0.3, 0.3, 0.2) ) # library(ggplot2) and then he creates some limits from the se variables. limits <- aes(ymax = resp + se, ymin=resp - se) [elements omitted] # and then he creates the plot (I'm interested in). p <- ggplot(df, aes(colour=group, y=resp, x=trt)) p + geom_line(aes(group=group)) + geom_errorbar(limits, width=0.2) I can (of course) get Hadley's example to run, but I can't do it on my data as I don't have a 'se' variable/don't know how to create it. I have a group variable, a treatment variable, and a response variable, but no se variable. Could anyone out there explain how I create a 'se' variable in my data? I'm sure my reasoning is the one that is off, and not ggplot2 (I'm a big fan). Your help is appreciated! Thanks, Eric
Can't anybody give me a hint on how to solve this? I even bought the ggplot2-book, so you could also give a page (or a series of pages). Thanks, Eric On Thu, Feb 17, 2011 at 10:19 AM, Eric Fail <eric.fail at gmx.com> wrote:> > Dear R-list > > I'm working with with geom_errorbar; specifically I'm trying to > reproduce the example Hadley Wickham have on > http://had.co.nz/ggplot2/geom_errorbar.html (all in the button of the > page) where he makes an nice plot with errorbars and then draw lines > between the points. > > What confuses me is the 'limits' he defines for the errorbars from the > se variable. > > First he creates a dataset, > > df <- data.frame( > ?trt = factor(c(1, 1, 2, 2)), > ?resp = c(1, 5, 3, 4), > ?group = factor(c(1, 2, 1, 2)), > ?se = c(0.1, 0.3, 0.3, 0.2) > ) > > # library(ggplot2) > > and then he creates some limits from the se variables. > > limits <- aes(ymax = resp + se, ymin=resp - se) > > [elements omitted] > > # and then he creates the plot (I'm interested in). > > p <- ggplot(df, aes(colour=group, y=resp, x=trt)) > p + geom_line(aes(group=group)) + geom_errorbar(limits, width=0.2) > > I can (of course) get Hadley's example to run, but I can't do it on my > data as I don't have a 'se' variable/don't know how to create it. I > have a group variable, a treatment variable, and a response variable, > but no se variable. > > Could anyone out there explain how I create a 'se' variable in my data? > > I'm sure my reasoning is the one that is off, and not ggplot2 (I'm a big fan). > > Your help is appreciated! > > Thanks, > Eric
Hi Scott, Thank you for taking the time to look at my problem! I played around with your example and realized that in solving the problem with limits by summarizing the data I loose the option to split the data along some third variable, say the 'color' variable in the diamonds data. Any idea on how I can solve the problem directly in ggplot2? Any ggplot2-expects out there? Sincerely, Eric On Sat, Feb 19, 2011 at 4:51 PM, Scott Chamberlain <myrmecocystus at gmail.com> wrote:> require(ggplot2) > > data(diamonds) > > diamonds <- diamonds[1:100,c(2,7)] > > # use ddply in plyr package (loaded with ggplot2) to get data to plot > > diamonds_df <- ddply(diamonds, .(cut), summarise, > > mean_price = mean(price), > > se_price = sd(price)/sqrt(length(price)) > > ) > > limits <- aes(ymax = mean_price + se_price, ymin = mean_price - se_price) > > ggplot(diamonds_df, aes(x = cut, y = mean_price)) + > > geom_point() + > > geom_errorbar(limits, width=0.2) > > Sincerely, > > Scott Chamberlain > > Rice University, EEB Dept. > > On Saturday, February 19, 2011 at 3:12 PM, Eric Fail wrote: > > Can't anybody give me a hint on how to solve this? I even bought the > ggplot2-book, so you could also give a page (or a series of pages). > > Thanks, > Eric > > On Thu, Feb 17, 2011 at 10:19 AM, Eric Fail <eric.fail at gmx.com> wrote: > > Dear R-list > > I'm working with with geom_errorbar; specifically I'm trying to > reproduce the example Hadley Wickham have on > http://had.co.nz/ggplot2/geom_errorbar.html (all in the button of the > page) where he makes an nice plot with errorbars and then draw lines > between the points. > > What confuses me is the 'limits' he defines for the errorbars from the > se variable. > > First he creates a dataset, > > df <- data.frame( > ?trt = factor(c(1, 1, 2, 2)), > ?resp = c(1, 5, 3, 4), > ?group = factor(c(1, 2, 1, 2)), > ?se = c(0.1, 0.3, 0.3, 0.2) > ) > > # library(ggplot2) > > and then he creates some limits from the se variables. > > limits <- aes(ymax = resp + se, ymin=resp - se) > > [elements omitted] > > # and then he creates the plot (I'm interested in). > > p <- ggplot(df, aes(colour=group, y=resp, x=trt)) > p + geom_line(aes(group=group)) + geom_errorbar(limits, width=0.2) > > I can (of course) get Hadley's example to run, but I can't do it on my > data as I don't have a 'se' variable/don't know how to create it. I > have a group variable, a treatment variable, and a response variable, > but no se variable. > > Could anyone out there explain how I create a 'se' variable in my data? > > I'm sure my reasoning is the one that is off, and not ggplot2 (I'm a big > fan). > > Your help is appreciated! > > Thanks, > Eric > > ______________________________________________ > 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. > >
Thank you Scott and Ista,
I really appreciate your help! I solved it with Scott's help on the ddply.
For the record, here is the working example that solves my initial question:
## install.packages(c("ggplot2", "plyr"))
require(ggplot2)
data(diamonds)
diamonds <- diamonds[1:100,c(2,7)]
# use ddply in plyr package (loaded with ggplot2) to get data to plot
diamonds_df <- ddply(diamonds, .(cut, color), summarise,
mean_price = mean(price),
se_price = sd(price)/sqrt(length(price))
)
limits <- aes(ymax = mean_price + se_price, ymin = mean_price - se_price)
ggplot(diamonds_df, aes(colour= color, x = cut, y = mean_price)) +
geom_point() +
geom_line(aes(group= color)) +
geom_errorbar(limits, width=0.2)
Very grateful!
Eric
On Sat, Feb 19, 2011 at 6:17 PM, Scott Chamberlain
<myrmecocystus at gmail.com> wrote:> Hi Eric,
> I would just include that third variable in the ddply call, for example:
> ddply(diamonds, .(cut, clarity, etc...), summarise,
> mean =?mean(price,
> se = ...
> )
> where you can summarise by multiple variables within the ".(x, y,
etc.)"\\
> I think that answers your question. Let me know if not. The example I sent
> earlier was just for simplicity.
> Scott
>
> On Saturday, February 19, 2011 at 4:58 PM, Eric Fail wrote:
>
> Hi Scott,
>
> Thank you for taking the time to look at my problem!
>
> I played around with your example and realized that in solving the
> problem with limits by summarizing the data I loose the option to
> split the data along some third variable, say the 'color' variable
in
> the diamonds data.
>
> Any idea on how I can solve the problem directly in ggplot2? Any
> ggplot2-expects out there?
>
> Sincerely,
> Eric
>
>
> On Sat, Feb 19, 2011 at 4:51 PM, Scott Chamberlain
> <myrmecocystus at gmail.com> wrote:
>
> require(ggplot2)
>
> data(diamonds)
>
> diamonds <- diamonds[1:100,c(2,7)]
>
> # use ddply in plyr package (loaded with ggplot2) to get data to plot
>
> diamonds_df <- ddply(diamonds, .(cut), summarise,
>
> mean_price = mean(price),
>
> se_price = sd(price)/sqrt(length(price))
>
> )
>
> limits <- aes(ymax = mean_price + se_price, ymin = mean_price -
se_price)
>
> ggplot(diamonds_df, aes(x = cut, y = mean_price)) +
>
> geom_point() +
>
> geom_errorbar(limits, width=0.2)
>
> Sincerely,
>
> Scott Chamberlain
>
> Rice University, EEB Dept.
>
> On Saturday, February 19, 2011 at 3:12 PM, Eric Fail wrote:
>
> Can't anybody give me a hint on how to solve this? I even bought the
> ggplot2-book, so you could also give a page (or a series of pages).
>
> Thanks,
> Eric
>
> On Thu, Feb 17, 2011 at 10:19 AM, Eric Fail <eric.fail at gmx.com>
wrote:
>
> Dear R-list
>
> I'm working with with geom_errorbar; specifically I'm trying to
> reproduce the example Hadley Wickham have on
> http://had.co.nz/ggplot2/geom_errorbar.html (all in the button of the
> page) where he makes an nice plot with errorbars and then draw lines
> between the points.
>
> What confuses me is the 'limits' he defines for the errorbars from
the
> se variable.
>
> First he creates a dataset,
>
> df <- data.frame(
> ?trt = factor(c(1, 1, 2, 2)),
> ?resp = c(1, 5, 3, 4),
> ?group = factor(c(1, 2, 1, 2)),
> ?se = c(0.1, 0.3, 0.3, 0.2)
> )
>
> # library(ggplot2)
>
> and then he creates some limits from the se variables.
>
> limits <- aes(ymax = resp + se, ymin=resp - se)
>
> [elements omitted]
>
> # and then he creates the plot (I'm interested in).
>
> p <- ggplot(df, aes(colour=group, y=resp, x=trt))
> p + geom_line(aes(group=group)) + geom_errorbar(limits, width=0.2)
>
> I can (of course) get Hadley's example to run, but I can't do it on
my
> data as I don't have a 'se' variable/don't know how to
create it. I
> have a group variable, a treatment variable, and a response variable,
> but no se variable.
>
> Could anyone out there explain how I create a 'se' variable in my
data?
>
> I'm sure my reasoning is the one that is off, and not ggplot2 (I'm
a big
> fan).
>
> Your help is appreciated!
>
> Thanks,
> Eric
>
> ______________________________________________
> 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.
>
>