Forgot to cc to list
Hi Luigi
Our emails are apparently crossing
What you are doing is referencing down ONLY to the stimulation level and not
the stimulation level + productivity level required for each of the N and P
groups
notch<-0.3
stripplot(
copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
"ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
my.data,
group = positivity,
hor=F,
layout = c(8,1),
scales = list(x = list(at = c(1,2), labels = c("N","P"))),
jitter.data=TRUE, pch=c(16,1), col="black",
ylab=expression(bold("Copy")),
xlab=expression(bold("Stimulation")),
main="Plot",
par.settings = list(strip.background=list(col="white")),
par.strip.text=list(font=2),
key = key.plot,
panel = function(x, y, ...)
{
pnl = panel.number()
for (i in 1:2){
datme<-subset(datmeA, positivity==i-1)
w<-i+k
panel.segments(x0 = X[w], y0 = datme[datme[,2]==
levels(datme[,2])[pnl],"copy"],
x1 = X[w+1], y1 = datme[datme[,2]==
levels(datme[,2])[pnl],"copy"],lwd = 2, col = "black")
k=k+1
panel.stripplot(x,y, ...)
panel.stripplot(x,y, ...)
}
}
)
for (i in 1:2){
datme<-subset(datmeA, positivity==i-1)
w<-i+k
panel.segments(x0 = X[w], y0 = datme[datme[,2]==
levels(datme[,2])[pnl],"copy"],
x1 = X[w+1], y1 = datme[datme[,2]==
levels(datme[,2])[pnl],"copy"],lwd = 2, col = "black")
k=k+1
panel.stripplot(x,y, ...)
the more lattice way is
notch<-0.3
stripplot(
copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
"ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
my.data,
group = positivity,
hor=F,
layout = c(8,1),
scales = list(x = list(at = c(1,2), labels = c("N","P"))),
jitter.data=TRUE, pch=c(16,1), col="black",
ylab=expression(bold("Copy")),
xlab=expression(bold("Stimulation")),
main="Plot",
par.settings = list(strip.background=list(col="white")),
par.strip.text=list(font=2),
key = key.plot,
panel = panel.superpose,
panel.groups = function(x, y, group.number, ...) {
panel.segments(x0= x-notch, x1=x+notch, y0=mean(y),
y1=mean(y), lty = c(1:2)[group.number],
lwd=c(2:1)[group.number], col = c(1:2)[group.number])
panel.stripplot(x,y, ...)
}
)
Duncan
-----Original Message-----
From: Luigi Marongiu [mailto:marongiu.lu...@gmail.com]
Sent: Wednesday, 30 April 2014 02:44
To: Duncan Mackay
Subject: Re: [R] lattice plot formatting: pch, abbreviation and labels
Dear Duncan,
I think the solution is close by. I can now plot the segments directly
with stripplot using a vector containing the required positions; the
only problem is to generate 4 consecutive indeces using two nested
loops -- using the subtraction of the index and a number I obtained
the duplication of the values, as you can see in the second example.
Many thanks,
Luigi
X<-c(0.7, 1.3, 1.7, 2.3)
stripplot(
copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
"ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
my.data,
group = positivity,
hor=F,
layout = c(8,1),
scales = list(x = list(at = c(1,2), labels = c("N","P"))),
jitter.data=TRUE, pch=c(16,1), col="black",
ylab=expression(bold("Copy")),
xlab=expression(bold("Stimulation")),
main="Plot",
par.settings = list(strip.background=list(col="white")),
par.strip.text=list(font=2),
key = key.plot,
panel = function(x, y, ...)
{
pnl = panel.number()
for (i in 1:2){
datme<-subset(datmeA, positivity==i-1)
k<-i-1
for (j in 1:2)
{
panel.segments(x0 = X[k+j], y0 = datme[datme[,2]==
levels(datme[,2])[pnl],"copy"],
x1 = X[k+j+1], y1 =
datme[datme[,2]== levels(datme[,2])[pnl],"copy"],lwd = 2, col =
c("magenta","grey"))
}
panel.stripplot(x,y, ...)
}
}
)
#### this approach gives duplications:
notch<-0.3
stripplot(
copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
"ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
my.data,
group = positivity,
hor=F,
layout = c(8,1),
scales = list(x = list(at = c(1,2), labels = c("N","P"))),
jitter.data=TRUE, pch=c(16,1), col="black",
ylab=expression(bold("Copy")),
xlab=expression(bold("Stimulation")),
main="Plot",
par.settings = list(strip.background=list(col="white")),
par.strip.text=list(font=2),
key = key.plot,
panel = function(x, y, ...)
{
pnl = panel.number()
for (i in 1:2){
datme<-subset(datmeA, positivity==i-1)
k<-i-1
for (j in 1:2)
{
panel.segments(x0 = j-notch, y0 =
datme[datme[,2]== levels(datme[,2])[pnl],"copy"],
x1 = j+notch, y1 =
datme[datme[,2]== levels(datme[,2])[pnl],"copy"],lwd = 2, col =
c("magenta","grey"))
}
panel.stripplot(x,y, ...)
}
}
)
On Tue, Apr 29, 2014 at 10:26 AM, Duncan Mackay <dulca...@bigpond.com> wrote:
> Hi Luigi
>
> Only minor changes needed.
>
> When you go back to a normal xyplot the rules of ratio variables apply the
> x-axis default in your case something like pretty(range(x)
> So the x-axis limits range from 0-1
> and the panel limits therefore are 0-1 +/- 4%
> With strip stripplot being categorical the limits are for values 1 and 2 so
> the top value for 2 is not being shown
> (easily seen with str(xyplot object))
>
> You missed out the assigning of groups to the segments.
> You could do this by a for loop of 1:2 or by using groups/panel.groups.
> I have not got the time to dig out the code to do it at the moment.
>
> xyplot(copy ~ positivity|stimulation, data = my.data,
> group = factor(positivity),
> as.table = TRUE,
> layout = c(8,1),
> xlim = c(-1,2),
> scales = list(x = list(at = c(0,1),
> labels = c("N","P"),
> rot = 0)),
> jitter.data=TRUE,
> pch=c(16,1),
> col="black",
> ylab=expression(bold("Copy")),
> xlab=expression(bold("Stimulation")),
> main="Plot",
> par.settings = list(strip.background=list(col="white")),
> par.strip.text=list(font=2),
> key = list(space="top",
> columns=2,
> text=list(c("Positive", "Negative"), col="black"),
> points=list(pch=c(16,1), col="black")),
> panel = function(x, y,...){
> pnl = panel.number()
> #panel.abline(h = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"ratio"], col = c("red","black"), lty=3)
> #for (j in 1:2){
> # with(subset(datmeA, (positivity == j-1 & stimulation ==
> levels(datmeA$stimulation)[pnl])),
> # panel.abline(h = copy, lwd = 1, col =
> c("red","black")[j], lty = 1) )
> for (j in 1:2){
> panel.segments(x0 = (j-1)-0.25, y0 = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"copy"], # amend to copy
> x1 = (j-1)+0.25, y1 = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"copy"],
> lwd = 2, col = c("magenta","grey")[j])
> }
>
> panel.stripplot(x,y, ...)
> }
> )
> If you wanted full N P then
>
> scales = list(x = list(at = c(0,1),
> alternating = F,
> labels = c("Negative","Positive"),
> rot = 90)), # rot = 0 if labels as before
>
> Duncan
>
> -----Original Message-----
> From: Luigi Marongiu [mailto:marongiu.lu...@gmail.com]
> Sent: Tuesday, 29 April 2014 04:34
> To: Duncan Mackay
> Subject: Re: [R] lattice plot formatting: pch, abbreviation and labels
>
> Dear Duncan,
> sorry to pester you again with this, but probably the solution is
> getting closer. following one of your previous tips i could write the
> xyplot synthax as you suggested:
>
> library(lattice)
> my.data<-structure(list(
> column_1 = 1:120,
> column_2 = structure(c(
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8), .Label = c("Unst.", "ESAT6", "CFP10", "Rv3615c",
> "Rv2654", "Rv3879", "Rv3873", "PHA"), class = "factor"),
> column_3 = structure(c(
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 0,0,0,0,0,0,0,0)),
> column_4 = c(
>
> 192.0519108,183.6403531,53.46798757,83.60638077,69.60749873,159.4706861,256.8765622,499.2899303,
>
> 2170.799076,1411.349719,2759.472348,2098.973397,2164.739515,1288.676574,1611.486543,6205.229575,
>
> 870.7424981,465.9967135,191.8962375,864.0937485,2962.693675,1289.259137,2418.651212,7345.712517,
> 0,168.1198893,674.4342961,101.1575401,47.81596237,0,0,1420.793922,
>
> 142.6871331,5.466468742,291.9564635,80.73914133,73.02239621,64.47806871,144.3543635,3167.959757,
>
> 3164.748333,1092.634557,28733.20269,1207.87783,729.6090973,151.8706088,241.2466141,9600.963594,
>
> 1411.718287,12569.96285,1143.254476,6317.378481,16542.27718,79.68025792,1958.495138,7224.503437,
>
> 208.4382941,69.48609769,656.691151,0.499017582,7114.910926,187.6296174,41.73980805,8930.784541,
>
> 4.276752185,0.432300363,60.89228665,1.103924786,0.490686366,1.812993239,7.264531581,1518.610307,
>
> 2172.051528,595.8513744,17141.84336,589.6565971,1340.287628,117.350942,593.7034054,24043.61463,
>
> 0,81.83292179,1539.864321,36.41722958,8.385131047,161.7647376,65.21615696,7265.573875,
>
> 97.84753179,154.051827,0.613835842,10.06138851,45.04879285,176.8284258,18795.75462,30676.769,
>
> 5780.34957,944.2200834,2398.235596,1083.393165,2541.714557,1251.670895,1547.178549,1792.679176,
>
> 3067.988416,8117.210173,23676.02226,8251.937547,17360.80494,18563.61561,16941.865,31453.96708,
>
> 2767.493803,4796.33016,12292.93705,3864.657567,9380.673835,14886.44683,8457.88646,26050.47191)),
> .Names = c("row", "stimulation", "positivity", "copy"), row.names =
> c(NA, -120L),
> class = "data.frame")
>
> key.plot<-list(
> space="top", columns=2,
> text=list(c("Positive", "Negative"), col="black"),
> points=list(pch=c(16,1), col="black"))
>
> datmeA <- aggregate(copy ~ positivity+stimulation, my.data, median, na.rm = T)
>
>
> #### HERE IS THE IMPORTANT BIT ###
>
> xyplot(copy ~ positivity|stimulation,
> my.data,
> group = positivity,
> hor=F,
> as.table = TRUE,
> layout = c(8,1),
> scales = list(x = list(alternating = FALSE, at = c(0.2,0.8), labels
> = c("P","N"))),
> pch=c(16,1), col="black",
> ylab=expression(bold("Copy")),
> xlab=expression(bold("Stimulation")),
> main="Plot",
> par.settings = list(strip.background=list(col="white")),
> par.strip.text=list(font=2),
> key = list(space="top", columns=2, text=list(c("Positive",
> "Negative"), col="black"), points=list(pch=c(16,1), col="black")),
> panel = function(x, y, ...){
> pnl = panel.number()
> panel.segments(x0 = x-0.25, y0 = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"ratio"],
> x1 = x+0.25, y1 = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"ratio"],
> lwd = 2, col = c("magenta","grey"))
> panel.stripplot(x,y, ...)
> }
> )
>
> ############################
>
> beside beign less elegant than stripplot() -- there is no jittering
> and requires the positions for the labels -- there are mainly two
> problems:
> 1. the dots are too close to the margins -- I tried to use the 'at'
> argument but it did not work
> 2. the segments are replicated -- there should be a 'panel.group'
> somewhere but I obtained a lot of errors when I tried to place it.
>
> Wouldn't be easier to use the stripplot directly, using maybe a factor
> to place the segments? I tried to place the panel.function in
> stripplot but it did not work at all...
>
> stripplot(copy ~ factor(positivity)|factor(stimulation, levels =
> c("Unst.", "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879",
> "Rv3873","PHA")),
> my.data,
> group = positivity,
> hor=F,
> layout = c(8,1),
> scales = list(x = list(at = c(1,2), labels = c("N","P"))),
> jitter.data=TRUE, pch=c(16,1), col="black",
> ylab=expression(bold("Copy")),
> xlab=expression(bold("Stimulation")),
> main="Plot",
> par.settings = list(strip.background=list(col="white")),
> par.strip.text=list(font=2),
> key = list(space="top", columns=2, text=list(c("Positive",
> "Negative"), col="black"), points=list(pch=c(16,1), col="black")),
> panel = function(x, y, ...){
> pnl = panel.number()
> panel.segments(x0 = x-0.25, y0 = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"ratio"],
> x1= x+0.25, y1 =
> datmeA[datmeA[,2]== levels(datmeA[,2])[pnl],"ratio"],
> lwd = 2, col = c("magenta","grey"))
> panel.stripplot(x,y, ...)
> }
> )
>
>
> Best wishes,
> Luigi
>
> On Mon, Apr 28, 2014 at 2:25 AM, Duncan Mackay <dulca...@bigpond.com> wrote:
>> Hi Luigi
>>
>> Here are 2 ways of doing it.
>>
>> The first is a "cheats" way ie easy.
>>
>> The second is a substitute for the proper way who's code eludes me at the
>> moment. I changed the lty on the ablines as it appears confusing and as you
>> are bolding it seems more appropriate. A better way may be to change 1 line
>> type.
>>
>> stripplot(copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
>> "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
>> my.data,
>> group = positivity,
>> hor=F,
>> layout = c(8,1),
>> scales = list(x = list(at = c(1,2), labels = c("N","P"))),
>> jitter.data=TRUE, pch=c(16,1), col="black",
>> ylab=expression(bold("Copy")),
>> xlab=expression(bold("Stimulation")),
>> main="Plot",
>> par.settings = list(strip.background=list(col="white")),
>> par.strip.text=list(font=2),
>> key = list(space="top",
>> columns=2,
>> text=list(c("Positive", "Negative"), col="black"),
>> points=list(pch=c(16,1), col="black")),
>> panel = function(x, y,...){
>> pnl = panel.number()
>> #panel.abline(h = datmeA[datmeA[,2]==
>> levels(datmeA[,2])[pnl],"ratio"], col = c("red","black"), lty=3)
>>
>> panel.average(x, y, fun = mean, horizontal = F, lty = 3,
>> col.line = c("red","black"), type = "l")
>>
>> panel.stripplot(x,y, ...)
>> }
>> )
>>
>> stripplot(copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
>> "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
>> my.data,
>> group = positivity,
>> hor=F,
>> layout = c(8,1),
>> scales = list(x = list(at = c(1,2), labels = c("N","P"))),
>> jitter.data=TRUE, pch=c(16,1), col="black",
>> ylab=expression(bold("Copy")),
>> xlab=expression(bold("Stimulation")),
>> main="Plot",
>> par.settings = list(strip.background=list(col="white")),
>> par.strip.text=list(font=2),
>> key = list(space="top",
>> columns=2,
>> text=list(c("Positive", "Negative"), col="black"),
>> points=list(pch=c(16,1), col="black")),
>> panel = function(x, y,...){
>> pnl = panel.number()
>> #panel.abline(h = datmeA[datmeA[,2]==
>> levels(datmeA[,2])[pnl],"ratio"], col = c("red","black"), lty=3)
>> for (j in 1:2){
>> with(subset(datmeA, (positivity == j-1 & stimulation ==
>> levels(datmeA$stimulation)[pnl])),
>> panel.abline(h = copy, lwd = 1, col =
>> c("red","black")[j], lty = 1) )
>>
>> }
>>
>> panel.stripplot(x,y, ...)
>> }
>> )
>>
>> Remember abline and panel.abline etc only take 1 line at a time so if you
>> have more than 1 group you have 2 call it more than once
>>
>> Regards
>> Duncan
>>
>> -----Original Message-----
>> From: Luigi Marongiu [mailto:marongiu.lu...@gmail.com]
>> Sent: Monday, 28 April 2014 04:03
>> To: Duncan Mackay
>> Subject: Re: [R] lattice plot formatting: pch, abbreviation and labels
>>
>> Dear Duncan,
>> may I bother you a bit more with the same data set? I would like now
>> to add a segment corresponding to the median values, as we discussed
>> antecedently.
>> I have tried to use the code you wrote in the previous mails, but it
>> hasn't worked. First I have found the aggregate medians values and
>> assigned to datmeA, then pasted the code you wrote, but without
>> success. Would be possible to substitute the panel.abline with
>> panel.segments? but in this case how to tell lattice what are the
>> values for "N" or "P"?
>> Best wishes,
>> Luigi
>>
>> CODE::::
>> library(lattice)
>>
>> my.data<-structure(list(
>> column_1 = 1:120,
>> column_2 = structure(c(
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8), .Label = c("Unst.", "ESAT6", "CFP10", "Rv3615c",
>> "Rv2654", "Rv3879", "Rv3873", "PHA"), class = "factor"),
>> column_3 = structure(c(
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 0,0,0,0,0,0,0,0)),
>> column_4 = c(
>>
>> 192.0519108,183.6403531,53.46798757,83.60638077,69.60749873,159.4706861,256.8765622,499.2899303,
>>
>> 2170.799076,1411.349719,2759.472348,2098.973397,2164.739515,1288.676574,1611.486543,6205.229575,
>>
>> 870.7424981,465.9967135,191.8962375,864.0937485,2962.693675,1289.259137,2418.651212,7345.712517,
>> 0,168.1198893,674.4342961,101.1575401,47.81596237,0,0,1420.793922,
>>
>> 142.6871331,5.466468742,291.9564635,80.73914133,73.02239621,64.47806871,144.3543635,3167.959757,
>>
>> 3164.748333,1092.634557,28733.20269,1207.87783,729.6090973,151.8706088,241.2466141,9600.963594,
>>
>> 1411.718287,12569.96285,1143.254476,6317.378481,16542.27718,79.68025792,1958.495138,7224.503437,
>>
>> 208.4382941,69.48609769,656.691151,0.499017582,7114.910926,187.6296174,41.73980805,8930.784541,
>>
>> 4.276752185,0.432300363,60.89228665,1.103924786,0.490686366,1.812993239,7.264531581,1518.610307,
>>
>> 2172.051528,595.8513744,17141.84336,589.6565971,1340.287628,117.350942,593.7034054,24043.61463,
>>
>> 0,81.83292179,1539.864321,36.41722958,8.385131047,161.7647376,65.21615696,7265.573875,
>>
>> 97.84753179,154.051827,0.613835842,10.06138851,45.04879285,176.8284258,18795.75462,30676.769,
>>
>> 5780.34957,944.2200834,2398.235596,1083.393165,2541.714557,1251.670895,1547.178549,1792.679176,
>>
>> 3067.988416,8117.210173,23676.02226,8251.937547,17360.80494,18563.61561,16941.865,31453.96708,
>>
>> 2767.493803,4796.33016,12292.93705,3864.657567,9380.673835,14886.44683,8457.88646,26050.47191)),
>> .Names = c("row", "stimulation", "positivity", "copy"), row.names =
>> c(NA, -120L),
>> class = "data.frame")
>>
>>
>> key.plot<-list(
>> space="top", columns=2,
>> text=list(c("Positive", "Negative"), col="black"),
>> points=list(pch=c(16,1), col="black"))
>>
>> datmeA <- aggregate(copy ~ positivity+stimulation, my.data, median, na.rm =
>> T)
>>
>> stripplot(
>> copy ~ factor(positivity)|factor(stimulation,
>> levels = c("Unst.", "ESAT6","CFP10","Rv3615c", "Rv2654",
>> "Rv3879", "Rv3873","PHA")),
>> group = positivity,
>> my.data,
>> hor=F,
>> layout = c(8,1),
>> scales = list(x = list(at = c(1,2), labels = c("N","P"))),
>> jitter.data=TRUE, pch=c(16,1), col="black",
>> ylab=expression(bold("Copy")),
>> xlab=expression(bold("Stimulation")), main="Plot",
>> par.settings = list(strip.background=list(col="white")),
>> par.strip.text=list(font=2),
>> key = key.plot,
>> panel = function(x, y){
>> pnl = panel.number()
>> panel.abline(h = datmeA[datmeA[,2]==
>>
>> levels(datmeA[,2])[pnl],"ratio"], col = c("red","black"), lty=3)
>>
>> panel.stripplot(x,y, ...)
>> }
>> )
>>
>> On Sun, Apr 27, 2014 at 2:06 AM, Duncan Mackay <dulca...@bigpond.com> wrote:
>>> Hi Luigi
>>>
>>> You are typing things unnecessarily: do not use the attach command unless
>>> absolutely necessary - it has unfortunate consequences.
>>> It is better to use with or within.
>>> alpha is not available with some devices with bad consequences if used; its
>>> default is 1 anyway.
>>>
>>> Once you have stated a data.frame as the data object it is usually not
>>> necessary to use the data.frame$ sign in to signify column names: use the
>>> column names.
>>> data = "a data.frame" is the equivalent to with
>>>
>>> You are reordering the levels of stimulation and changing the name of 1 so I
>>> thought it was easiest to make a column stim and do things there otherwise
>>> it the relevelling could be done in the data argument using the subset
>>> argument. Then the change to "Unst" could be done by using strip =
>>> strip.custom(factor.levels = ...),
>>>
>>> To change for the -/+ I made a group - the easiest way.
>>> Have a look a changing the negative symbol to 20 or something else as it is
>>> hard to visualise. You may vary things with changing cex (remember to have 2
>>> values 1 for each group).
>>>
>>> If you do str(xyplot object) you will get a big print of the object and
>>> within that the x limits are shown as "0", "1" which means that the x values
>>> are 1 and 2
>>> There is a command to get these things but I have forgotten it
>>>
>>> my.data$stimulation <- factor(levels = c("Unstimulated",
>>> "ESAT6","CFP10","Rv3615c","Rv2654", "Rv3879", "Rv3873","PHA"))
>>> my.data$stim <- factor(my.data$stimulation, labels = c("Unst.",
>>> "ESAT6","CFP10","Rv3615c","Rv2654", "Rv3879", "Rv3873","PHA"))
>>> my.data$pos <- ifelse(sign(my.data$copy) > 0, 2,1)
>>>
>>> stripplot(copy ~ factor(positivity)|stim,my.data,
>>> groups = pos,
>>> hor = F,
>>> layout = c(8,1),
>>> scales = list(x = list(at = c(1,2),
>>> labels = c("N","P"))),
>>> jitter.x = TRUE,
>>> amount = 2,
>>> pch = c(16,1),
>>> col = "black",
>>> ylab = expression(bold("Copy")),
>>> xlab = expression(bold("Stimulation")),
>>> main="Plot",
>>> par.settings = list(strip.background=list(col="white")),
>>> par.strip.text=list(font=2)
>>> )
>>>
>>> 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-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
>>> Behalf Of Luigi Marongiu
>>> Sent: Sunday, 27 April 2014 02:07
>>> To: r-help@r-project.org
>>> Subject: [R] lattice plot formatting: pch, abbreviation and labels
>>>
>>> Dear all,
>>> I am trying to use the lattice plot, but the syntax is quite
>>> difficult. Specifically I have eight variables (1 to 8) each of them
>>> further subdivided in two classes (negative=0 and positive=1). I am
>>> using the stripplot() to represent these values. I would like to
>>> represent the negative and positive values with black and white dots
>>> so I have tried to use the argument pch=c(16, 1) both in the main
>>> stripplot function and embedded in the scale argument. However the
>>> resulting plot shows that some points are drawn with the pch=16 and
>>> other with pch=1 irrespective of their class.
>>> Is there a way to draw the values for the variable positivity = 0 with
>>> pch=16 and those with positivity = 1 with pch=0?
>>>
>>> In addition I would like to change the labels under the axis from 0,1
>>> to N,P. However when I placed labels=c("N", "P") or labels=list("N",
>>> "P") in the main stripplot() I did not obtained any difference and
>>> when placed within the scale argument also the -labels were modified.
>>> Is there a way to change the label 0 with N and the label 1 with P?
>>>
>>> final problem: I would like to abbreviate the "Unstimulated" box label
>>> with "Unst.". I have tried the abbreviate=TRUE argument but again the
>>> syntax is too complex for me and it did not work.
>>> Is there a way to abbreviate the variables names?
>>>
>>> Thank you very much for your help.
>>> Best wishes,
>>> Luigi
>>>
>>>
>>> CODE:::::::::
>>>
>>>
>>> ### open plot library
>>> library(lattice)
>>>
>>> my.data<-structure(list(
>>> column_1 = 1:120,
>>> column_2 = structure(c(
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8), .Label = c("Unstimulated", "ESAT6", "CFP10",
>>> "Rv3615c", "Rv2654", "Rv3879", "Rv3873", "PHA"), class = "factor"),
>>> column_3 = structure(c(
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 0,0,0,0,0,0,0,0)),
>>> column_4 = c(
>>>
>>> 192.0519108,183.6403531,53.46798757,83.60638077,69.60749873,159.4706861,256.
>>> 8765622,499.2899303,
>>>
>>> 2170.799076,1411.349719,2759.472348,2098.973397,2164.739515,1288.676574,1611
>>> .486543,6205.229575,
>>>
>>> 870.7424981,465.9967135,191.8962375,864.0937485,2962.693675,1289.259137,2418
>>> .651212,7345.712517,
>>> 0,168.1198893,674.4342961,101.1575401,47.81596237,0,0,1420.793922,
>>>
>>> 142.6871331,5.466468742,291.9564635,80.73914133,73.02239621,64.47806871,144.
>>> 3543635,3167.959757,
>>>
>>> 3164.748333,1092.634557,28733.20269,1207.87783,729.6090973,151.8706088,241.2
>>> 466141,9600.963594,
>>>
>>> 1411.718287,12569.96285,1143.254476,6317.378481,16542.27718,79.68025792,1958
>>> .495138,7224.503437,
>>>
>>> 208.4382941,69.48609769,656.691151,0.499017582,7114.910926,187.6296174,41.73
>>> 980805,8930.784541,
>>>
>>> 4.276752185,0.432300363,60.89228665,1.103924786,0.490686366,1.812993239,7.26
>>> 4531581,1518.610307,
>>>
>>> 2172.051528,595.8513744,17141.84336,589.6565971,1340.287628,117.350942,593.7
>>> 034054,24043.61463,
>>>
>>> 0,81.83292179,1539.864321,36.41722958,8.385131047,161.7647376,65.21615696,72
>>> 65.573875,
>>>
>>> 97.84753179,154.051827,0.613835842,10.06138851,45.04879285,176.8284258,18795
>>> .75462,30676.769,
>>>
>>> 5780.34957,944.2200834,2398.235596,1083.393165,2541.714557,1251.670895,1547.
>>> 178549,1792.679176,
>>>
>>> 3067.988416,8117.210173,23676.02226,8251.937547,17360.80494,18563.61561,1694
>>> 1.865,31453.96708,
>>>
>>> 2767.493803,4796.33016,12292.93705,3864.657567,9380.673835,14886.44683,8457.
>>> 88646,26050.47191)),
>>> .Names = c("row", "stimulation", "positivity", "copy"), row.names =
>>> c(NA, -120L),
>>> class = "data.frame")
>>> attach(my.data)
>>>
>>> stripplot(my.data$copy ~
>>> factor(my.data$positivity)|factor(my.data$stimulation,
>>> levels = c("Unstimulated", "ESAT6","CFP10","Rv3615c",
>>> "Rv2654", "Rv3879", "Rv3873","PHA")),
>>> my.data, hor=F, layout = c(8,1), scales = list(relation =
>>> "same"),
>>> jitter.data=TRUE, alpha=1, pch=c(16,1), col="black",
>>> ylab=expression(bold("Copy")),
>>> xlab=expression(bold("Stimulation")), main="Plot",
>>> par.settings = list(strip.background=list(col="white")),
>>> par.strip.text=list(font=2))
>>>
>>> ______________________________________________
>>> R-help@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.
>>>
>>
>
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
