[R] high density plots using lattice dotplot()
Duncan Mackay
dulcalma at bigpond.com
Thu Apr 23 04:08:41 CEST 2015
Hi Luigi
Try
set.seed(1)
PLATE <-
data.frame(Delta.Rn = rnorm(500),
Cycle = rnorm(500),
Delta2 = rnorm(500)+1,
Well = rep(1:50, each = 10))
head(PLATE,10)
xyplot(Delta.Rn+Delta2 ~ Cycle | Well,
data = subset(PLATE, Well %in% 1:49),
allow.multiple = TRUE,
ylab="Fluorescence (Delta Rn)",
xlab="Cycles",
main="TITLE",
scales = list(
x = list(draw = FALSE),
y = list(draw = FALSE),
relation="same",
alternating=TRUE),
as.table = TRUE,
layout = c(10,5),
par.settings = list(
strip.background=list(col="white"),
# layout.heights = list(strip = 0.8),
axis.text = list(cex = 0.6),
par.xlab.text = list(cex = 0.75),
par.ylab.text = list(cex = 0.75),
par.main.text = list(cex = 0.8),
superpose.symbol = list(pch = ".", cex = 2,
col = c(2,4) )
),
strip = FALSE,
type = "p",
key = list(text = list(label = c("Delta.Rn","Delta2")),
points = list(cex = 0.6, pch = 16, col = c(2,4)),
cex = 0.6,
x = 0.9,
y = 0.1),
panel = panel.superpose,
panel.groups = function(x,y,...){
panel.xyplot(x,y,... )
# text argument can be a vector of values not
# necessarily the group name
pnl = panel.number() # needed as group.number if added is now either 1 or 2
grid.text(c(LETTERS,letters)[pnl],
y = 0.93, x = 0.5,
default.units = "npc",
just = c("left", "bottom"),
gp = gpar(fontsize = 7) )
}
)
Remember to delete the group argument (I forgot to at first as the groups are now Delta.Rn Delta2)
You may have 1+ empty panels so put the legend there where ever it is just amend the x and y or fine tune them
you can have the pch = "." and increase cex but it will become as square with large cex
Duncan
-----Original Message-----
From: Luigi Marongiu [mailto:marongiu.luigi at gmail.com]
Sent: Thursday, 23 April 2015 10:05
To: Duncan Mackay
Subject: Re: [R] high density plots using lattice dotplot()
Dear Duncan,
sorry to come back so soon, but i wanted to ask you whether it would
be possible to plot two sets of lines within each box, let's say a
main value A and a secondary value B. In normal plots I could use a
plot() followed by points(); what would be the strategy here?
Thank you again,
best regards,
Luigi
On Wed, Apr 22, 2015 at 6:46 AM, Duncan Mackay <dulcalma at bigpond.com> wrote:
>
> Hi Luigi
>
> I should have made up an example to make things easier when I replied today
>
> This should get you going
>
> set.seed(1)
>
> PLATE <-
> data.frame(Delta.Rn = rnorm(500),
> Cycle = rnorm(500),
> Well = rep(1:50, each = 10))
> head(PLATE)
>
> xyplot(Delta.Rn ~ Cycle | Well,
> data = PLATE,
> groups = Well,
> ylab="Fluorescence (Delta Rn)",
> xlab="Cycles",
> main="TITLE",
> scales = list(
> x = list(draw = FALSE),
> y = list(draw = FALSE),
> relation="same",
> alternating=TRUE),
> as.table = TRUE,
> layout = c(10,5),
> par.settings = list(
> strip.background=list(col="white"),
> # layout.heights = list(strip = 0.8),
> axis.text = list(cex = 0.6),
> par.xlab.text = list(cex = 0.75),
> par.ylab.text = list(cex = 0.75),
> par.main.text = list(cex = 0.8)
> superpose.symbol = list(pch = ".", cex = 2)
> ),
> strip = FALSE,
> type = "p",
> col = 1,
> panel = panel.superpose,
> panel.groups = function(x,y,...,group.number){
>
> panel.xyplot(x,y,... )
>
> # text argument can be a vector of values not
> # necessarily the group name
> grid.text(c(LETTERS,letters)[group.number],
> y = 0.93, x = 0.5,
> default.units = "npc",
> just = c("left", "bottom"),
> gp = gpar(fontsize = 7) )
>
> }
> )
>
> You could use panel.text instead of grid.text
> Duncan
>
> -----Original Message-----
> From: Luigi Marongiu [mailto:marongiu.luigi at gmail.com]
> Sent: Wednesday, 22 April 2015 08:24
> To: Duncan Mackay
> Subject: Re: [R] high density plots using lattice dotplot()
>
> Dear Duncan,
> thank you for your reply. I tried to implement your suggestions but as
> is on your reply did not work (actually R crashed) and a slight
> elaboration returned the figure attached, which is essentially still
> displaying text and not drawing the data. Here is what I wrote:
>
> xyplot(Delta.Rn ~ Cycle | Well,
> data = PLATE,
> ylab="Fluorescence (Delta Rn)",
> xlab="Cycles",
> main=TITLE,
> scales = list(
> x = list(draw = FALSE),
> y = list(draw = FALSE),
> relation="same",
> alternating=TRUE),
> as.table = TRUE,
> layout = c(24,16),
> par.settings = list(
> strip.background=list(col="white"),
> axis.text = list(cex = 0.6),
> par.xlab.text = list(cex = 0.75),
> par.ylab.text = list(cex = 0.75),
> superpose.symbol = list(pch = ".", cex = 2)
> ),
> strip = FALSE,
> type = "p",
> layout.heights = list(strip = 0.8),
> panel = function(x,y, subscripts, groups,...){
> panel.superpose(x,y,subscripts,groups,...,
> col = ...)
> panel.text(x,y,...,cex = 0.6)
> }
> )
>
>
> How can I improve the script?
> Many thanks
> Luigi
>
> On Tue, Apr 21, 2015 at 12:35 AM, Duncan Mackay <dulcalma at bigpond.com> wrote:
>> Hi Luigi
>>
>> Strips take up space so if you are willing to not have strip and put the
>> strip values within the plot area then
>>
>> xyplot(y ~ x|cond.factor, data = ...,
>> as.table = T,
>> groups = ...,
>> layout = ...,
>> drop.unused = T,
>> par.settings = list(axis.text = list(cex = 0.6),
>> par.xlab.text = list(cex = 0.75),
>> par.ylab.text = list(cex = 0.75)
>> superpose.symbol = list(pch = ".", cex = 2)
>> ),
>> strip = FALSE,
>> scales = list(x = list(alternating = 2),
>> y = list(alternating = FALSE)
>> ),
>> type = "p",
>> panel = function(x,y, subscripts, groups,...){
>> panel.superpose(x,y,subscripts,groups,...,
>> col = ...)
>> panel.text(x,y,...,cex = 0.6)
>> }
>> )
>>
>> if the text values are a vector
>> stext = ...
>> xyplot(y ~ x|cond.factor, data = ...,
>> as.table = T,
>> groups = ...,
>> layout = ...,
>> drop.unused = T,
>> par.settings = list(axis.text = list(cex = 0.6),
>> par.xlab.text = list(cex = 0.75),
>> par.ylab.text = list(cex = 0.75)
>> superpose.symbol = list(pch = ".", cex = 2)
>> ),
>> strip = FALSE,
>> scales = list(x = list(alternating = 2),
>> y = list(alternating = FALSE)
>> ),
>> type = "p",
>> panel = function(x,y, subscripts, groups,...){
>> pnl = panel.number()
>> panel.superpose(x,y,subscripts,groups,...,
>> col = ...)
>> panel.text(x,y,stext[pnl],cex = 0.6)
>> }
>> )
>>
>> you could also you group.number instead of pnl if it is needed elsewhere.
>> text position could be done in a similar fashion if needed to be in
>> different places for some panels.
>>
>> If you require the strip then an additional par.settings is
>> layout.heights = list(strip = 0.8)
>> or even untested in this situation
>> strip = FALSE
>> strip.left = TRUE
>>
>> Regards
>>
>> Duncan
>>
>> Duncan Mackay
>> Department of Agronomy and Soil Science
>> University of New England
>> Armidale NSW 2351
>> Email: home: mackay at northnet.com.au
>>
>> -----Original Message-----
>> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Luigi
>> Marongiu
>> Sent: Sunday, 19 April 2015 19:28
>> To: r-help
>> Subject: [R] high density plots using lattice dotplot()
>>
>> Dear all,
>> I am trying to plot the results of a PCR experiments that involves 384
>> individual plots. Admittedly the space for the plots will be tiny, but
>> I just nedd some icon to have a feeling of the layout of the
>> experiment and a quick comparison of the plots.
>> I believe that lattice would be the right tool, but when I tried to
>> implement i got an error. Specifically the output would be a A4 pdf,
>> so with about 600 cm2 of drawing space, which gives about 1.5 cm2 for
>> each plot; removing the labels that might just work.
>> So I have the y values = 'fluorescence', x 'values' = cycles and 384
>> 'well' data. I implemented to begin with:
>>
>> xyplot(fluorescence ~ cycles | well,
>> ylab="Fluorescence",
>> xlab="Cycles",
>> main=list(draw = FALSE),
>> scales = list(
>> x = list(draw = FALSE),
>> y = list(draw = FALSE),
>> relation="same",
>> alternating=TRUE),
>> layout = c(24,16),
>> par.settings = list(strip.background=list(col="white")),
>> pch = "."
>> )
>>
>> but the the individual graphs show only the writing "data" instead of
>> the actual plots.
>> How can I overcome this error?
>> Thank you
>> Best regards
>> Luigi
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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>>
>
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