[FORGED] Re: single strip for the same group in dotplot lattice
Hi
The following is a bit customised to your example, but maybe if there's
no other way ...
library(grid)
## Go down to the viewport that lays everything out
downViewport("plot_01.toplevel.vp")
## Eyeball the widths and heights (the "null"s are the plot regions)
## current.viewport()$layout$widths
## current.viewport()$layout$heights
## Make a viewport along the top strips and draw in it
pushViewport(viewport(layout.pos.col=7:25,
layout.pos.row=8))
grid.rect(y=1, height=unit(1, "lines"), just="top",
gp=gpar(fill="paleturquoise"))
grid.text("run_2", y=unit(1, "npc") - unit(.5, "lines"))
upViewport()
## Make a viewport along the bottom strips and draw in it
pushViewport(viewport(layout.pos.col=7:25,
layout.pos.row=12))
grid.rect(y=1, height=unit(1, "lines"), just="top",
gp=gpar(fill="paleturquoise"))
grid.text("run_1", y=unit(1, "npc") - unit(.5, "lines"))
upViewport()
Paul
On 23/02/17 22:00, Luigi Marongiu wrote:
Dear Duncan and Philip, thank you for your answers. maybe the toy data I gave it is a bit too easy, so I am attaching a new dataset with 5 targets. As you can see from it, now there are 5 panel strips with the label "run_1" and 5 with the label "run_2". What I would like to do is to merge those with the same label so to have only two labels "run_1" and "run_2". the examples from Duncan contains plenty of keys but I think make the reading of the plot more difficult; most of the plots have only one strip. thank you luigi
# the values are actually repeated, but they are just for example
cluster <- c(rep("run_1", 45), rep("run_2", 45))
type <- rep(c("blank", "positive", "negative"),30)
target <- rep(c(rep("A", 3), rep("B", 3), rep("C", 3), rep("D", 3),
rep("E", 3)), 6)
value <- rep(c(rnorm(1, mean=0.001, sd=0.1), rnorm(1, mean=2, sd=1),
rnorm(1, mean=1, sd=1)),30)
my.data <- data.frame(cluster, type, target, value)
library(lattice)
dotplot(
value ~ type|target + cluster,
my.data,
groups = type,
pch=21,
main = "Luminex analysis MTb humans",
xlab = "Target", ylab = "Reading",
col = c("grey", "green", "red"),
par.settings = list(strip.background = list(col="paleturquoise")),
scales = list(alternating = FALSE, x = list(labels = c("", "", ""))),
key = list(
space = "top",
columns = 3,
text = list(c("Blank", "Negative", "Positive"), col="black"),
rectangles = list(col=c("grey", "green", "red"))
)
)
On Thu, Feb 23, 2017 at 2:50 AM, Duncan Mackay <dulcalma at bigpond.com> wrote:
Hi Liugi
Here are some ideas quickly
4 panels diagonals are blank
mdata = my.data
mdata$ct <- paste(target, "Run", rep(1:2, each = 6))
mdata$typeT <- paste(mdata$target,mdata$type)
dotplot(
value ~ type|ct,
mdata2,
groups = typeT,
par.settings = list(strip.background = list(col="paleturquoise"),
superpose.symbol = list(col = c(2:4),
pch = rep(c(1,20),each =
3))),
# type
scales = list(alternating = FALSE, x = list(labels = c("", "", ""))),
main = "Luminex analysis MTb humans",
xlab = "Target",
ylab = "Reading",
auto.key = T,
panel = panel.superpose
)
# for when the 4 panels have plots not 2 as now
mdata2 = mdata
mdata2$target = rep(LETTERS[2:1], ea=6)
mdata2$value= mdata2$value+0.1
mdata2 <- rbind(mdata,mdata2)
mdata2$typeT <- paste(mdata2$target,mdata2$type)
dotplot(
value ~ type|target + cluster,
mdata2,
groups = typeT,
par.settings = list(strip.background = list(col="paleturquoise"),
superpose.symbol = list(col = c(2:4),
pch = rep(c(1,20),each =
3))), # type
scales = list(alternating = FALSE, x = list(labels = c("", "", ""))),
main = "Luminex analysis MTb humans",
xlab = "Target",
ylab = "Reading",
auto.key = T,
panel = panel.superpose
)
dotplot(
value ~ type|ct,
mdata2,
groups = typeT,
par.settings = list(strip.background = list(col="paleturquoise"),
superpose.symbol = list(col = c(2:4),
pch = rep(c(1,20),each =
3))), # type
scales = list(alternating = FALSE, x = list(labels = c("", "", ""))),
main = "Luminex analysis MTb humans",
strip = strip.custom(factor.levels = paste("Run",1:2),
par.strip.text = list(cex = 1) ),
xlab = "Target",
ylab = "Reading",
auto.key = T,
panel = panel.superpose
)
dotplot(
value ~ type|cluster,
mdata2,
groups = typeT,
par.settings = list(strip.background = list(col="paleturquoise"),
superpose.symbol = list(col = c(2:4),
pch = rep(c(1,20),each =
3))),
# type
scales = list(alternating = FALSE, x = list(labels = c("", "", ""))),
main = "Luminex analysis MTb humans",
xlab = "Target",
ylab = "Reading",
auto.key = T,
panel = panel.superpose
)
Regards
Duncan
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Luigi
Marongiu
Sent: Wednesday, 22 February 2017 21:26
To: P Tennant; r-help
Subject: Re: [R] single strip for the same group in dotplot lattice
Dear Philip,
the data is indeed a toy data: the real one will have 15 panels (=targets)
and two or three clusters. this means that I will have 15 strips with the
label "run 1" = "cluster 1" etc. the point of the toy data is that I get a
4x4 panel plot with 8 strips labelled "run 1", "run 2", "A" and "B". What I
am looking for is to collapse the strips so to get only one label "run 1"
and only one with "run 2" in order to simplify the plot. Hope this helps.
Thanks
Luigi
On Wed, Feb 22, 2017 at 9:53 AM, P Tennant <philipt900 at iinet.net.au>
wrote:
Hi Luigi, I'm afraid I don't understand your toy data as you've described it, but
if
you really don't have run 2 for target A, and don't have run 1 for target B, why not just create another factor that reflects this, and plot that? my.data$clus2 <- with(my.data, interaction(cluster, target)) and call: dotplot(value ~ type| clus2, ... ) Philip On 22/02/2017 8:03 PM, Luigi Marongiu wrote:
dear all, I have a set of data that is subdivided in cluster (run 1/run 2) and in target (A/B). When plotting, I obtain a panel strip with "run 1" and
"run
2" for each "A" and "B" panel, so "run 1" appears twice and so does "run 2". It is possible to merge the strip together so that I will have "run
1"
or "run 2" only once? this will reduce the complexity of the data and
allow
more space for more detailed information in the strip.
the data follows,
thank you
L
cluster<- c(rep("run_1", 6), rep("run_2", 6))
type<- rep(c("blank", "positive", "negative"),2)
target<- c(rep("A", 6), rep("B", 6))
value<- c(0.01, 1.1, 0.5,
0.02, 1.6, 0.8,
0.07, 1.4, 0.7,
0.03, 1.4, 0.4)
my.data<- data.frame(cluster, type, target, value)
library(lattice)
dotplot(
value ~ type|target + cluster,
my.data,
groups = type,
pch=21,
main = "Luminex analysis MTb humans",
xlab = "Target", ylab = "Reading",
col = c("grey", "green", "red"),
par.settings = list(strip.background = list(col="paleturquoise")),
scales = list(alternating = FALSE, x = list(labels = c("", "", ""))),
key = list(
space = "top",
columns = 3,
text = list(c("Blank", "Negative", "Positive"), col="black"),
rectangles = list(col=c("grey", "green", "red"))
)
)
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Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 paul at stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/