R help - Oct 2009 - Problem using with panel.average in Lattice package

Hi,

I'm having a problem getting the panel.average function to work as I
expect it to in a lattice plot. I wish to draw lines between the
averages of groups of y-values at specific x-values. I have created a
dataset below which is similar to my real data. I also show an example
of using panel.loess in place of panel.average; it performs in a
manner similar to what I want panel.average to do except it shows a
loess line rather than a straight line connecting the means of the
groups.

Please see my coded examples, below.

Regards,
Mark Dalphin

================================================================My system
information:
> library(lattice)
> print(sessionInfo())
R version 2.9.1 (2009-06-26) 
i686-pc-linux-gnu 

locale:
LC_CTYPE=en_NZ.UTF-8;LC_NUMERIC=C;LC_TIME=en_NZ.UTF-8;LC_COLLATE=en_NZ.UTF-8;
LC_MONETARY=C;LC_MESSAGES=en_NZ.UTF-8;LC_PAPER=en_NZ.UTF-8;LC_NAME=C;
LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_NZ.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lattice_0.17-25

loaded via a namespace (and not attached):
[1] grid_2.9.1  tools_2.9.1

##--------------------------------------------------------------
## This dataset is too complicated, but it does show the type of plot I want.
##
## Create a fake qPCR dataset: Eight 96-well plates over 4 days (2 per day),
## 2 genes per plate (multiplexed), and 4 "Hi" positive control and
## 4 "Lo" positive controls per plate.
## Create the experimental data; by rights it is all identical, expect for
## experimental errors with in days and between days.
## For this simulation, each gene will be given a base value.
## In qPCR the higher the "Ct" value, the lower the concentration.
library(lattice)  # Add for ease of cut-n-paste of this code
date  <- c('2009-09-07', '2009-09-08', '2009-09-10',
'2009-09-14')
probe <- c('Gene.A1', 'Gene.A2', 'Gene.B1',
'Gene.B2')
conc  <- c('Lo', 'Hi')
base.lo	<- c(Gene.A1=29, Gene.A2=25, Gene.B1=28, Gene.B2=31)
base.hi <- base.lo - 8
day.err <- c(Day.1=0, Day.2=1, Day.3=1.5, Day.4=1.0)

d <- data.frame()
for(i in seq(along=date)) {
    for(j in seq(along=probe)) {
        for(k in seq(along=conc)) {
	    d <- rbind(d, data.frame(Date=rep(date[i], length=4),
                                     Probe=rep(probe[j], length=4),
                                     Conc=rep(conc[k], length=4),
                                     Ct=rnorm(4, sd=0.5) + (k-1)*8 + base.hi[j]
+ day.err[i]
                                     ))
        }
    }
}
d$Date <- as.POSIXct(d$Date)

##--------------------------------------------------
## Example 1
## Print with LOESS line showing the 'means' for the groups.
## This is close, but I don't want a loess line; I want straight lines
## between mean values.
print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
             panel="panel.superpose",	  
             panel.groups=function(x, y, ...) {
                 panel.loess(x, y, ...)
                 panel.xyplot(x, y, ...)
             },
             auto.key=TRUE))

##--------------------------------------------------
## Example 2
## Parallel construction to the loess example, above.
## Note the loss of the lines. The 'horizontal' default
## is different between 'panel.loess' and 'panel.average'.
print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
             panel="panel.superpose",
             panel.groups=function(x, y, ...) {
                 panel.average(x, y, horizontal=FALSE, ...)
                 panel.xyplot(x, y, ...)
             },
             auto.key=TRUE))

##--------------------------------------------------
## Example 3
## Don't pass along the '...' to the panel.average. Now I
## get lines, but not matching colours to the points.
print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
             panel="panel.superpose",
             panel.groups=function(x, y, ...) {
                 panel.average(x, y, horizontal=FALSE)
                 panel.xyplot(x, y, ...)
             },
             auto.key=TRUE))

##**********************************************************************
Main question:

I want to create a plot that looks like Example 3, but with the
coloured lines of Example 1. Suggestions? I've looked in RSiteSearch()
for both "panel.average" and "panel.linejoin" but found
nothing addressing
this.

Side question:

I also read the source code to panel.average, panel.loess and
panel.superpose.  Which leads to a side question; how do I determine
what parameters are being passed within '...'? I tried recreating my
panel.groups function above as an explicit (non-anonymous) function
and using debug() on it, but running formals() within that debugging session
didn't seem to show me the huge list of arguments from
panel.superpose, "do.call(panel.groups, args)", coming into my panel
function. Is there some way to "see" these arguments?

##**********************************************************************

On Fri, Oct 2, 2009 at 8:03 PM, Mark Dalphin <mark.dalphin at peblnz.com>
wrote:
> Hi,
>
> I'm having a problem getting the panel.average function to work as I
> expect it to in a lattice plot. I wish to draw lines between the
> averages of groups of y-values at specific x-values. I have created a
> dataset below which is similar to my real data. I also show an example
> of using panel.loess in place of panel.average; it performs in a
> manner similar to what I want panel.average to do except it shows a
> loess line rather than a straight line connecting the means of the
> groups.
>
> Please see my coded examples, below.
>
> Regards,
> Mark Dalphin
>
> ================================================================> My
system information:
>
>> library(lattice)
>> print(sessionInfo())
>
> R version 2.9.1 (2009-06-26) i686-pc-linux-gnu
> locale:
>
LC_CTYPE=en_NZ.UTF-8;LC_NUMERIC=C;LC_TIME=en_NZ.UTF-8;LC_COLLATE=en_NZ.UTF-8;
> LC_MONETARY=C;LC_MESSAGES=en_NZ.UTF-8;LC_PAPER=en_NZ.UTF-8;LC_NAME=C;
> LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_NZ.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
> other attached packages:
> [1] lattice_0.17-25
>
> loaded via a namespace (and not attached):
> [1] grid_2.9.1 ?tools_2.9.1
>
> ##--------------------------------------------------------------
> ## This dataset is too complicated, but it does show the type of plot I
> want.
> ##
> ## Create a fake qPCR dataset: Eight 96-well plates over 4 days (2 per
day),
> ## 2 genes per plate (multiplexed), and 4 "Hi" positive control
and
> ## 4 "Lo" positive controls per plate.
> ## Create the experimental data; by rights it is all identical, expect for
> ## experimental errors with in days and between days.
> ## For this simulation, each gene will be given a base value.
> ## In qPCR the higher the "Ct" value, the lower the
concentration.
> library(lattice) ?# Add for ease of cut-n-paste of this code
> date ?<- c('2009-09-07', '2009-09-08',
'2009-09-10', '2009-09-14')
> probe <- c('Gene.A1', 'Gene.A2', 'Gene.B1',
'Gene.B2')
> conc ?<- c('Lo', 'Hi')
> base.lo <- c(Gene.A1=29, Gene.A2=25, Gene.B1=28, Gene.B2=31)
> base.hi <- base.lo - 8
> day.err <- c(Day.1=0, Day.2=1, Day.3=1.5, Day.4=1.0)
>
> d <- data.frame()
> for(i in seq(along=date)) {
> ? for(j in seq(along=probe)) {
> ? ? ? for(k in seq(along=conc)) {
> ? ? ? ? ? ?d <- rbind(d, data.frame(Date=rep(date[i], length=4),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Probe=rep(probe[j], length=4),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Conc=rep(conc[k], length=4),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Ct=rnorm(4, sd=0.5) + (k-1)*8 +
> base.hi[j] + day.err[i]
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?))
> ? ? ? }
> ? }
> }
> d$Date <- as.POSIXct(d$Date)
>
> ##--------------------------------------------------
> ## Example 1
> ## Print with LOESS line showing the 'means' for the groups.
> ## This is close, but I don't want a loess line; I want straight lines
> ## between mean values.
> print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
> ? ? ? ? ? ?panel="panel.superpose",
> ?panel.groups=function(x, y, ...) {
> ? ? ? ? ? ? ? ?panel.loess(x, y, ...)
> ? ? ? ? ? ? ? ?panel.xyplot(x, y, ...)
> ? ? ? ? ? ?},
> ? ? ? ? ? ?auto.key=TRUE))
>
> ##--------------------------------------------------
> ## Example 2
> ## Parallel construction to the loess example, above.
> ## Note the loss of the lines. The 'horizontal' default
> ## is different between 'panel.loess' and 'panel.average'.
> print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
> ? ? ? ? ? ?panel="panel.superpose",
> ? ? ? ? ? ?panel.groups=function(x, y, ...) {
> ? ? ? ? ? ? ? ?panel.average(x, y, horizontal=FALSE, ...)
> ? ? ? ? ? ? ? ?panel.xyplot(x, y, ...)
> ? ? ? ? ? ?},
> ? ? ? ? ? ?auto.key=TRUE))
Unfortunately, the implicit type="p" argument in panel.superpose is
overriding the type="l" in panel.average (may be it should be
unmodifiable). So, you need

print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
             panel="panel.superpose",
             panel.groups=function(x, y, ..., type) {
                 panel.average(x, y, ..., type = "l", horizontal =
FALSE)
                 panel.xyplot(x, y, ..., type = type)
             },
             auto.key=TRUE))

It's more common to use the syntactic sugar provided by panel.xyplot:

print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
             type = c("p", "a"),
             auto.key=TRUE))

>
> ##--------------------------------------------------
> ## Example 3
> ## Don't pass along the '...' to the panel.average. Now I
> ## get lines, but not matching colours to the points.
> print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
> ? ? ? ? ? ?panel="panel.superpose",
> ? ? ? ? ? ?panel.groups=function(x, y, ...) {
> ? ? ? ? ? ? ? ?panel.average(x, y, horizontal=FALSE)
> ? ? ? ? ? ? ? ?panel.xyplot(x, y, ...)
> ? ? ? ? ? ?},
> ? ? ? ? ? ?auto.key=TRUE))
>
> ##**********************************************************************
> Main question:
>
> I want to create a plot that looks like Example 3, but with the
> coloured lines of Example 1. Suggestions? I've looked in RSiteSearch()
> for both "panel.average" and "panel.linejoin" but found
nothing addressing
> this.
>
> Side question:
>
> I also read the source code to panel.average, panel.loess and
> panel.superpose. ?Which leads to a side question; how do I determine
> what parameters are being passed within '...'? I tried recreating
my
> panel.groups function above as an explicit (non-anonymous) function
> and using debug() on it, but running formals() within that debugging
session
> didn't seem to show me the huge list of arguments from
> panel.superpose, "do.call(panel.groups, args)", coming into my
panel
> function. Is there some way to "see" these arguments?
I usually put in

str(list(...))

in the function. For interactive debugging, you could have

dots <- list(...)

and then debug.

-Deepayan