R help - Nov 2010 - How do I order xyplot line points?

I have the following xyplot figure:

  http://img577.imageshack.us/img577/686/filesizeresults12000000.png

The data are organized in a matrix file as follows:

  Type	Elements	Chromosome	Time
  bedGz	12000000	chr1	14.240
  bedGz	12000000	chr2	7.949
  bedGz	12000000	chr3	5.103
  bedGz	12000000	chr4	5.290
  bedGz	12000000	chr5	5.161
  ...

The x-axis labels in the Chromosome column are ordered lexicographically in my
figure ( chr1 > chr10 > chr11 > ... ) ? this is correct.

However, the code I use to draw lines between points in the xyplot connects
points in numerical order ( chr1 > chr2 > ... ) ? this is incorrect.

The problem this causes is most evident in the line that is drawn for the blue
"bedGz" category.

What I would like is that categorical points are joined by lines in
lexicographic order, to match ordering of labels on the x-axis.

How do I modify the xyplot command so that the lines are joined in correct
order?

Here is the code I am using to draw my xyplot:

mtx <- read.table(mtxf.in, as.is=F, sep="\t", quote='',
header=T, stringsAsFactors=T)
attach(mtx)
postscript(mtxf.ps,
           width = 12,
           height = 6,
           paper = 'special',
           horizontal = F)
par(mar=c(0.0, 0.0, 0.0, 0.0))
mtx.p <- xyplot(Time~Chromosome|factor(Elements),
                mtx,
                type="o",
                groups=Type,
                col = c(
                  'red',
                  'green',
                  'red',
                  'green',
                  'blue'),
                auto.key=list(
                  lines=TRUE,
                  space="right"),
                ylab="CPU Time (sec)",
                xlab="Type",
                main="Extraction time for archive types")
print(mtx.p)
dev.off()    

Sorry if this is a dumb question. Thanks for your advice.

Regards,
Alex

Hi,

try this,

xyplot(Time~Chromosome|factor(Elements),
               data = mtx[order(mtx$Chromosome), ], ... [snipped])


HTH,

baptiste





On 7 November 2010 13:17, Alex Reynolds <reynolda at u.washington.edu>
wrote:
> I have the following xyplot figure:
>
> ?http://img577.imageshack.us/img577/686/filesizeresults12000000.png
>
> The data are organized in a matrix file as follows:
>
> ?Type ?Elements ? ? ? ?Chromosome ? ? ?Time
> ?bedGz 12000000 ? ? ? ?chr1 ? ?14.240
> ?bedGz 12000000 ? ? ? ?chr2 ? ?7.949
> ?bedGz 12000000 ? ? ? ?chr3 ? ?5.103
> ?bedGz 12000000 ? ? ? ?chr4 ? ?5.290
> ?bedGz 12000000 ? ? ? ?chr5 ? ?5.161
> ?...
>
> The x-axis labels in the Chromosome column are ordered lexicographically in
my figure ( chr1 > chr10 > chr11 > ... ) ? this is correct.
>
> However, the code I use to draw lines between points in the xyplot connects
points in numerical order ( chr1 > chr2 > ... ) ? this is incorrect.
>
> The problem this causes is most evident in the line that is drawn for the
blue "bedGz" category.
>
> What I would like is that categorical points are joined by lines in
lexicographic order, to match ordering of labels on the x-axis.
>
> How do I modify the xyplot command so that the lines are joined in correct
order?
>
> Here is the code I am using to draw my xyplot:
>
> mtx <- read.table(mtxf.in, as.is=F, sep="\t",
quote='', header=T, stringsAsFactors=T)
> attach(mtx)
> postscript(mtxf.ps,
> ? ? ? ? ? width = 12,
> ? ? ? ? ? height = 6,
> ? ? ? ? ? paper = 'special',
> ? ? ? ? ? horizontal = F)
> par(mar=c(0.0, 0.0, 0.0, 0.0))
> mtx.p <- xyplot(Time~Chromosome|factor(Elements),
> ? ? ? ? ? ? ? ?mtx,
> ? ? ? ? ? ? ? ?type="o",
> ? ? ? ? ? ? ? ?groups=Type,
> ? ? ? ? ? ? ? ?col = c(
> ? ? ? ? ? ? ? ? ?'red',
> ? ? ? ? ? ? ? ? ?'green',
> ? ? ? ? ? ? ? ? ?'red',
> ? ? ? ? ? ? ? ? ?'green',
> ? ? ? ? ? ? ? ? ?'blue'),
> ? ? ? ? ? ? ? ?auto.key=list(
> ? ? ? ? ? ? ? ? ?lines=TRUE,
> ? ? ? ? ? ? ? ? ?space="right"),
> ? ? ? ? ? ? ? ?ylab="CPU Time (sec)",
> ? ? ? ? ? ? ? ?xlab="Type",
> ? ? ? ? ? ? ? ?main="Extraction time for archive types")
> print(mtx.p)
> dev.off()
>
> Sorry if this is a dumb question. Thanks for your advice.
>
> Regards,
> Alex
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