Mulitple plotting in gplots

[troot]

"gplots" has a great function called plotmeans. I want to use this function to plot the means and CI of some grouped data (which is non-nomal) - I have done that.

However then I would then like to plot medians and CI's generated through bootstrapping and plot them on the same axes so I have two lines with points (mean and medians) each with CI's.

Is this possible?
How would I code to add the plot of medians etc on top of the plotmeans line?

Any help appreciated.

Regards

T

[bryangoodrich]

You can do this with base graphics by specifying your points (medians) and using segments and feeding them the medians plus/minus the CIs you calculate. Takes a few more lines than one boxed command, but it gives you that control you desire. I've only used gplots once, so I'm not familiar with its functions.

[Lazar]

I do not know the exact code but typically it would be something like:

plot1 <- ggplot (CODE  FOR MEANS and CIs)
plot2 <- plot1 + CODE FOR MEDIANS and CIs

something like stat_summary(fun.y = "median", geom = "line") might be what you need and median_hilow() will give you upper and lower quatiles.

PS the ggplot mailing list will give you exact (if not always polite) advice.

[Dason]

At first I immediately thought of ggplot2 as well. But they seem to be asking about gplots.

[Lazar]

oh right. Scratch that.

[troot]

Hi All
Thanks for the quick replies.
gplots has another function "plotCI" which looks promising.
I might try that before bryans advice.

On another note - iof I have a function that produces a plot( ie plotmeans in gplot) how can I get, view, extract the data points providing the plot???

Regards

S

[Dason]

It doesn't look like the plotmeans function has an option to return the calculated means. But it's easy enough to replicate that kind of behavior using the apply family of functions.

[bryangoodrich]

I know I have an example of plotting confidence intervals on my website. Check out chapters 2 or 3 in my ALSM project. Search for "segment" and you should find the code. Segments draws exactly that, a segment based on the start and end points you give. Your goal is simply to supply the start (the median) and the end point (median+CI radius). Since you should be able to calculate the median and CIs separately, you'll have all the data to produce your plot. Just do plot followed by segments with the appropriate inputs (see help pages). It's not as nice as a one-liner, but it really is at most like 4 lines.

[bugman]

Can't you just plot your means and create a new vector of your median values then use the add=T operator?

plotci will do this nicely!

Alternatively, I'd follow bryans advice and use the segments function in base.

[troot]

Hi bugman

If I use plotCI and want to add a another line of medians with+/- CI what form would the vector take??

[Dason]

You can always check the help file for plotCI

?plotCI

alternatively to see the examples provided in the help file in action you can use the example function

example(plotCI)