R help - Aug 2011 - Dot plot with two grouping variables concurrently

Dear R help(ers).  I'm an R-learner (about 10 hours now) trying to make a
ranked dot plot where the symbols are coded by two variables concurrently. 
I'm trying to use Deepanyan Sarkar's book 'Lattice' as a guide
but get the
feeling it is a  bit advanced for my level of understanding.  

I have three questions

Q1. 

Right now I like to know how to get the dual coding working on the points on
a dotplot and also annotate these in a key.  Specifically I'm attempting to
code the fill of the points by a variable called 'Commodity' but would
like
have different symbols to refelect a second variable called 'Year' (say
square, triangle and circle for different years).  

My code so far is as follows:

## initalise
library("lattice")

##read the data to a variable
Cal_dat <- read.table("Calibration2.dat",header = TRUE,sep =
"\t",)

## set up plotting colours for the fills 
col.pat<-c("violet","cyan","green","red","blue","black","yellow")

##set up the plot key to be inside the plot
plot.key<-list(
	corner=c(1,0),
	text=list(levels(Cal_dat$Commodity)),
	title="Ore type",
	points=list(pch=21,cex=1.3,fill=col.pat,col="black")
)	

##set some parameters for the dotplot
trellis.par.set(
 	dot.line=list(col = "transparent"),
	axis.line=list(col = "grey90"),
	axis.text=list(col ="grey50", cex=0.8),
	panel.background=list(col="grey98"),
	par.xlab.text= list(col="grey50")	
)

## Create the dot plot
dotplot(reorder(Mine, Resc_Gt)~ Resc_Gt,groups=Commodity,
      data=Cal_dat,
	cex=1.2, 
	pch=21,
	aspect=2.0,
	key=plot.key,
	col="black",
	fill=col.pat,
	origin=0,
	type = c("p", "h"),
	main = "Resource Tonnage",
	xlab= "tonnes (billions)"	
)

The dot plot so far is attached as well as the input data.

Q2

I'm puzzled by the waring message (below) I get when runnin the current code
as follows (What does this mean and why does it occur).

"Warning message:
In trellis.par.set(dot.line = list(col = "transparent"), axis.line
list(col = "grey90"),  :
  Note: The default device has been opened to honour attempt to modify
trellis settings"

Q3

Can anybody recommend a good 'starters' book for learning plotting in R
that
is reasonably clear on the basics.  My primary interest is the graphing
tools that are in lattice (hence trying the Deepayan Sarkar book), but I'm
finding this guide rather tough going.

Thanks in advance - MarkM

http://r.789695.n4.nabble.com/file/n3758248/Calibration2.dat
Calibration2.dat 
http://r.789695.n4.nabble.com/file/n3758248/Ranked_boxplot_by_commodity.png
Ranked_boxplot_by_commodity.png 

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Sent from the R help mailing list archive at Nabble.com.

> Q1.
>
> Right now I like to know how to get the dual coding working on the points
on
> a dotplot and also annotate these in a key. ?Specifically I'm
attempting to
> code the fill of the points by a variable called 'Commodity' but
would like
> have different symbols to refelect a second variable called 'Year'
(say
> square, triangle and circle for different years).
You can custumize pch as to reflect the levels of "Year" in both your
dotplot and key

my.pch<- 1:length(levels(Cal_dat$Year)) ### for example

Then, use my.pch in the places of  pch in your codes of dotplot and key

HTH

Weidong Gu
> My code so far is as follows:
>
> ## initalise
> library("lattice")
>
> ##read the data to a variable
> Cal_dat <- read.table("Calibration2.dat",header = TRUE,sep =
"\t",)
>
> ## set up plotting colours for the fills
>
col.pat<-c("violet","cyan","green","red","blue","black","yellow")
>
> ##set up the plot key to be inside the plot
> plot.key<-list(
> ? ? ? ?corner=c(1,0),
> ? ? ? ?text=list(levels(Cal_dat$Commodity)),
> ? ? ? ?title="Ore type",
> ? ? ? ?points=list(pch=21,cex=1.3,fill=col.pat,col="black")
> )
>
> ##set some parameters for the dotplot
> trellis.par.set(
> ? ? ? ?dot.line=list(col = "transparent"),
> ? ? ? ?axis.line=list(col = "grey90"),
> ? ? ? ?axis.text=list(col ="grey50", cex=0.8),
> ? ? ? ?panel.background=list(col="grey98"),
> ? ? ? ?par.xlab.text= list(col="grey50")
> )
>
> ## Create the dot plot
> dotplot(reorder(Mine, Resc_Gt)~ Resc_Gt,groups=Commodity,
> ? ? ?data=Cal_dat,
> ? ? ? ?cex=1.2,
> ? ? ? ?pch=21,
> ? ? ? ?aspect=2.0,
> ? ? ? ?key=plot.key,
> ? ? ? ?col="black",
> ? ? ? ?fill=col.pat,
> ? ? ? ?origin=0,
> ? ? ? ?type = c("p", "h"),
> ? ? ? ?main = "Resource Tonnage",
> ? ? ? ?xlab= "tonnes (billions)"
> )
>
> The dot plot so far is attached as well as the input data.
>
> Q2
>
> I'm puzzled by the waring message (below) I get when runnin the current
code
> as follows (What does this mean and why does it occur).
>
> "Warning message:
> In trellis.par.set(dot.line = list(col = "transparent"),
axis.line > list(col = "grey90"), ?:
> ?Note: The default device has been opened to honour attempt to modify
> trellis settings"
>
> Q3
>
> Can anybody recommend a good 'starters' book for learning plotting
in R that
> is reasonably clear on the basics. ?My primary interest is the graphing
> tools that are in lattice (hence trying the Deepayan Sarkar book), but
I'm
> finding this guide rather tough going.
>
> Thanks in advance - MarkM
>
> http://r.789695.n4.nabble.com/file/n3758248/Calibration2.dat
> Calibration2.dat
> http://r.789695.n4.nabble.com/file/n3758248/Ranked_boxplot_by_commodity.png
> Ranked_boxplot_by_commodity.png
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/Dot-plot-with-two-grouping-variables-concurrently-tp3758248p3758248.html
> Sent from the R help mailing list archive at Nabble.com.
>
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