On Fri, Oct 2, 2009 at 8:03 PM, Mark Dalphin <mark.dalp...@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
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