Re: [R] lattice plot formatting: pch, abbreviation and labels
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
Re: [R] lattice plot formatting: pch, abbreviation and labels
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
Re: [R] lattice plot formatting: pch, abbreviation and labels
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
Re: [R] lattice plot formatting: pch, abbreviation and labels
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
Re: [R] lattice plot formatting: pch, abbreviation and labels
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,
