Given my reproducible example
myexample<-structure(list(site = structure(c(4L, 2L, 2L, 4L, 2L, 4L, 4L,
3L, 1L, 3L, 1L, 1L, 3L, 4L, 5L, 2L), .Label = c("A", "B",
"C",
"D", "E"), class = "factor"), obs = c(0.302,
0.956, 0.72, 1.21,
0.887, 0.728, 1.294, 20.493, 0.902, 0.031, 0.468, 2.318, 4.795,
89.581, 4.59, 3618.353), sample = structure(c(6L, 6L, 2L, 8L,
7L, 7L, 9L, 4L, 4L, 1L, 1L, 3L, 3L, 10L, 11L, 5L), .Label =
c("18/08/2009",
"20/04/2009", "03/12/2008", "17/03/2009",
"05/01/2012", "21/04/2009",
"17/07/2009", "17/04/2009", "21/07/2009",
"29/01/2009", "16/07/2008"
), class = "factor", scores = structure(c(2, 3, 2, 3, 4, 4, 2,
5, 2, 4, 2), .Dim = 11L, .Dimnames = list(c("18/08/2009",
"21/04/2009",
"20/04/2009", "17/07/2009", "17/04/2009",
"21/07/2009", "03/12/2008",
"16/07/2008", "17/03/2009", "29/01/2009",
"05/01/2012"))))), .Names c("site",
"obs", "sample"), row.names = c(NA, -16L), class =
"data.frame")
I want to dotplot with lattice the observations (obs) against sampling dates
(sample) for each site but I need to reorder the factor levels of sampling
dates based on the value of observations within each site (rather than
keeping the original arbitrary data)
These are my two best (?) attempts both of them not properly working for
different reasons
#start
library(lattice); library(latticeExtra)
#first attempt
myexample$sample<-
with(myexample, reorder(sample,obs))
dotplot(sample ~ obs | site, data=myexample,
scales=list(x=list(log=TRUE), y=list(relation="free")),
xscale.components = xscale.components.logpower,
strip=FALSE, strip.left=TRUE, layout=c(1,5),
index.cond= function(x,y){median(x)},
panel = function(x,y,...) {
panel.dotplot(x,y,...)
panel.abline(v = median(x), col.line="red",
lty="dotted")
}
)
#second attempt
myexample$sample<-
with(myexample, reorder(reorder(sample,obs), as.numeric(site)))
dotplot(sample ~ obs | site, data=myexample,
scales=list(x=list(log=TRUE), y=list(relation="free")),
xscale.components = xscale.components.logpower,
strip=FALSE, strip.left=TRUE, layout=c(1,5),
index.cond= function(x,y){median(x)},
panel = function(x,y,...) {
panel.dotplot(x,y,...)
panel.abline(v = median(x), col.line="red",
lty="dotted")
}
)
#end
There is to note the presence of some ties (i.e. same sampling dates,
particularly noticeable for site A and B).
The number of factor levels related to sampling dates (11) is different than
total number of observations (17): is this responsible for the lack of
reordering for factor sample in the dotplot?
How to fix this ? How to get a neat y axis without that ?holes? in between
of the sampling dates within each site?
Should I try to make somehow as much factor levels as the observations so
that to avoid this sort of problem? Is there any alternative solution?
thank you
--
View this message in context:
http://r.789695.n4.nabble.com/Reordering-levels-of-a-factor-within-a-lattice-dotplot-tp4634201.html
Sent from the R help mailing list archive at Nabble.com.
Rui Barradas
2012-Jun-22 14:03 UTC
[R] Reordering levels of a factor within a lattice dotplot
Hello, Try the following myex <- myexample myex$sample <- as.character(myex$sample) myex$sample <- as.Date(myex$sample, format="%d/%m/%Y") myex Then, run the first attempt without bothering to order, lattice is clever and will do it for you. Hope this helps, Rui Barradas Em 22-06-2012 13:20, maxbre escreveu:> Given my reproducible example > > myexample<-structure(list(site = structure(c(4L, 2L, 2L, 4L, 2L, 4L, 4L, > 3L, 1L, 3L, 1L, 1L, 3L, 4L, 5L, 2L), .Label = c("A", "B", "C", > "D", "E"), class = "factor"), obs = c(0.302, 0.956, 0.72, 1.21, > 0.887, 0.728, 1.294, 20.493, 0.902, 0.031, 0.468, 2.318, 4.795, > 89.581, 4.59, 3618.353), sample = structure(c(6L, 6L, 2L, 8L, > 7L, 7L, 9L, 4L, 4L, 1L, 1L, 3L, 3L, 10L, 11L, 5L), .Label = c("18/08/2009", > "20/04/2009", "03/12/2008", "17/03/2009", "05/01/2012", "21/04/2009", > "17/07/2009", "17/04/2009", "21/07/2009", "29/01/2009", "16/07/2008" > ), class = "factor", scores = structure(c(2, 3, 2, 3, 4, 4, 2, > 5, 2, 4, 2), .Dim = 11L, .Dimnames = list(c("18/08/2009", "21/04/2009", > "20/04/2009", "17/07/2009", "17/04/2009", "21/07/2009", "03/12/2008", > "16/07/2008", "17/03/2009", "29/01/2009", "05/01/2012"))))), .Names > c("site", > "obs", "sample"), row.names = c(NA, -16L), class = "data.frame") > > > I want to dotplot with lattice the observations (obs) against sampling dates > (sample) for each site but I need to reorder the factor levels of sampling > dates based on the value of observations within each site (rather than > keeping the original arbitrary data) > > These are my two best (?) attempts both of them not properly working for > different reasons > > #start > > library(lattice); library(latticeExtra) > > #first attempt > myexample$sample<- > with(myexample, reorder(sample,obs)) > > > dotplot(sample ~ obs | site, data=myexample, > scales=list(x=list(log=TRUE), y=list(relation="free")), > xscale.components = xscale.components.logpower, > strip=FALSE, strip.left=TRUE, layout=c(1,5), > > index.cond= function(x,y){median(x)}, > > panel = function(x,y,...) { > panel.dotplot(x,y,...) > panel.abline(v = median(x), col.line="red", lty="dotted") > } > ) > > > #second attempt > myexample$sample<- > with(myexample, reorder(reorder(sample,obs), as.numeric(site))) > > > dotplot(sample ~ obs | site, data=myexample, > scales=list(x=list(log=TRUE), y=list(relation="free")), > xscale.components = xscale.components.logpower, > strip=FALSE, strip.left=TRUE, layout=c(1,5), > > index.cond= function(x,y){median(x)}, > > panel = function(x,y,...) { > panel.dotplot(x,y,...) > panel.abline(v = median(x), col.line="red", lty="dotted") > } > ) > > #end > > There is to note the presence of some ties (i.e. same sampling dates, > particularly noticeable for site A and B). > The number of factor levels related to sampling dates (11) is different than > total number of observations (17): is this responsible for the lack of > reordering for factor sample in the dotplot? > How to fix this ? How to get a neat y axis without that ?holes? in between > of the sampling dates within each site? > > Should I try to make somehow as much factor levels as the observations so > that to avoid this sort of problem? Is there any alternative solution? > > thank you > > > > -- > View this message in context: http://r.789695.n4.nabble.com/Reordering-levels-of-a-factor-within-a-lattice-dotplot-tp4634201.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Deepayan Sarkar
2012-Jun-23 06:03 UTC
[R] Reordering levels of a factor within a lattice dotplot
On Fri, Jun 22, 2012 at 5:50 PM, maxbre <mbressan at arpa.veneto.it> wrote:> Given my reproducible example > > myexample<-structure(list(site = structure(c(4L, 2L, 2L, 4L, 2L, 4L, 4L, > 3L, 1L, 3L, 1L, 1L, 3L, 4L, 5L, 2L), .Label = c("A", "B", "C", > "D", "E"), class = "factor"), obs = c(0.302, 0.956, 0.72, 1.21, > 0.887, 0.728, 1.294, 20.493, 0.902, 0.031, 0.468, 2.318, 4.795, > 89.581, 4.59, 3618.353), sample = structure(c(6L, 6L, 2L, 8L, > 7L, 7L, 9L, 4L, 4L, 1L, 1L, 3L, 3L, 10L, 11L, 5L), .Label = c("18/08/2009", > "20/04/2009", "03/12/2008", "17/03/2009", "05/01/2012", "21/04/2009", > "17/07/2009", "17/04/2009", "21/07/2009", "29/01/2009", "16/07/2008" > ), class = "factor", scores = structure(c(2, 3, 2, 3, 4, 4, 2, > 5, 2, 4, 2), .Dim = 11L, .Dimnames = list(c("18/08/2009", "21/04/2009", > "20/04/2009", "17/07/2009", "17/04/2009", "21/07/2009", "03/12/2008", > "16/07/2008", "17/03/2009", "29/01/2009", "05/01/2012"))))), .Names > c("site", > "obs", "sample"), row.names = c(NA, -16L), class = "data.frame") > > > I want to dotplot with lattice the observations (obs) against sampling dates > (sample) for each site but I need to reorder the factor levels of sampling > dates based on the value of observations ?within each site (rather than > keeping the original arbitrary data) > > These are my two best (?) attempts both of them not properly working for > different reasons > > #start > > library(lattice); library(latticeExtra) > > #first attempt > myexample$sample<- > ?with(myexample, reorder(sample,obs)) > > > dotplot(sample ~ obs | site, data=myexample, > ? ? ? ?scales=list(x=list(log=TRUE), y=list(relation="free")), > ? ? ? ?xscale.components = xscale.components.logpower, > ? ? ? ?strip=FALSE, strip.left=TRUE, layout=c(1,5), > > ? ? ? ?index.cond= function(x,y){median(x)}, > > ? ? ? ?panel = function(x,y,...) { > ? ? ? ? ?panel.dotplot(x,y,...) > ? ? ? ? ?panel.abline(v = median(x), col.line="red", lty="dotted") > ? ? ? ?} > ? ? ? ?) > > > #second attempt > myexample$sample<- > ?with(myexample, reorder(reorder(sample,obs), as.numeric(site))) > > > dotplot(sample ~ obs | site, data=myexample, > ? ? ? ?scales=list(x=list(log=TRUE), y=list(relation="free")), > ? ? ? ?xscale.components = xscale.components.logpower, > ? ? ? ?strip=FALSE, strip.left=TRUE, layout=c(1,5), > > ? ? ? ?index.cond= function(x,y){median(x)}, > > ? ? ? ?panel = function(x,y,...) { > ? ? ? ? ?panel.dotplot(x,y,...) > ? ? ? ? ?panel.abline(v = median(x), col.line="red", lty="dotted") > ? ? ? ?} > ? ? ? ?) > > #end > > There is to note the presence of some ties (i.e. same sampling dates, > particularly noticeable for site A and B). > The number of factor levels related to sampling dates (11) is different than > total number of observations (17): is this responsible for the lack of > reordering for factor sample in the dotplot? > How to fix this ? How to get a neat y axis without that ?holes? in between > of the sampling dates within each site? > > Should I try to make somehow as much factor levels as the observations so > that to avoid this sort of problem? Is there any alternative solution?Yes, you need to avoid duplicates. Here is one way to do that: myexample$sampleLabel <- as.character(myexample$sample) myexample$sampleId <- gl(length(myexample$sample), 1) myexample$sample2 <- with(myexample, reorder(reorder(sampleId, obs), as.numeric(site))) ## correct plot, but useless y-axis labels dotplot(sample2 ~ reorder(site, obs) | site, data = myexample, scales=list(x=list(log=TRUE), y=list(relation="free")), xscale.components = xscale.components.logpower, strip=FALSE, strip.left=TRUE, layout=c(1,5)) ## match reordered levels with original order, and set axis labels nl <- as.numeric(levels(myexample$sample2)) dotplot(sample2 ~ obs | reorder(site, obs), data = myexample, scales=list(x=list(log=TRUE), y=list(relation="free")), ylim = myexample$sampleLabel[nl], xscale.components = xscale.components.logpower, strip=FALSE, strip.left=TRUE, layout=c(1,5)) -Deepayan
thanks a lot deepayan, I will study carefully your code! thanks max -- View this message in context: http://r.789695.n4.nabble.com/Reordering-levels-of-a-factor-within-a-lattice-dotplot-tp4634201p4634277.html Sent from the R help mailing list archive at Nabble.com.