Hi Luigi
Michael answered your question about printing
lattice and ggplot require their graphics to be in print()
If you have problems in printing you may have to use
trellis.device(device = pdf, # or what ever the actual device is
file = ####,
<remainder of script>)
? trellis.device for info
I occasionally have to use it sometimes instead of pdf etc
Duncan
-----Original Message-----
From: Luigi Marongiu [mailto:marongiu.lu...@gmail.com]
Sent: Thursday, 23 April 2015 22:56
To: Duncan Mackay
Subject: Re: [R] high density plots using lattice dotplot()
Dear Duncan,
many thanks for the precious help! I have rearranged what you sent me
with a bit of stuff I wrote already for another project and the
results seems to work fine.
Best regards,
Luigi
>>> example
DF <-
data.frame(Y = rnorm(17280),
X = rnorm(1:45),
Y2 = rnorm(17280)+2,
Z = 1:384)
head(df,10)
xyplot(Y ~ X | Z,
data = DF,
groups = Z,
allow.multiple = TRUE,
ylab= "Y VALUES",
xlab="X VALUES",
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),
par.main.text = list(cex = 0.8),
superpose.symbol = list(type = "l", cex = 1)
),
strip = FALSE,
type = "l",
col = 3,
panel = panel.superpose
)
On Thu, Apr 23, 2015 at 3:08 AM, Duncan Mackay <dulca...@bigpond.com> wrote:
> 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.lu...@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 <dulca...@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.lu...@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 <dulca...@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: mac...@northnet.com.au
>>>
>>> -----Original Message-----
>>> From: R-help [mailto:r-help-boun...@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@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
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>
______________________________________________
R-help@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
and provide commented, minimal, self-contained, reproducible code.
