[R] set axis limit in lattice
Duncan Mackay
dulcalma at bigpond.com
Wed Apr 30 01:15:52 CEST 2014
Hi Luigi
This produces plenty of white space for the y axes
Y<-max(my.data$copy)
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")),
y= list(relation = "free")),
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()
k<-0
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, ...)
}
}
)
You could limit the y-axis to your levels
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")),
y= list(relation = "free",
limits = list(c(0, max panel 1),
c(0, max panel 2),
...
c(0, max panel 8)),
)),
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()
k<-0
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, ...)
}
}
)
Sorting the stimulation groups shows that some of them can be loosely grouped so reordering the factors
stripplot(copy ~ factor(positivity)|factor(stimulation, levels = c("PHA","Rv2654","CFP10","Unst.","Rv3615c", "Rv3873","ESAT6", "Rv3879")),
my.data,
group = positivity,
hor=F,
layout = c(2,4),
scales = list(x = list(at = c(1,2), labels = c("N","P")),
y= list(relation = "free")),
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()
k<-0
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, ...)
}
}
)
or using panel.groups
stripplot(copy ~ factor(positivity)|factor(stimulation, levels = c("PHA","Rv2654","CFP10","Unst.","Rv3615c", "Rv3873","ESAT6", "Rv3879")),
my.data,
group = positivity,
hor=F,
layout = c(2,4),
scales = list(x = list(at = c(1,2), labels = c("N","P")),
y= list(relation = "free")),
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-0.25, x1=x+0.25, 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, ...)
}
)
Regards
Duncan Mackay
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Luigi Marongiu
Sent: Wednesday, 30 April 2014 03:58
To: r-help at r-project.org
Subject: [R] set axis limit in lattice
Dear all,
I would like to set the axis of a figure using the max() so to have
more control on the limits of the axis -- this because in the actual
case more independent figures are generated from the same dataframe
and these must have the same axis scale.
Since the figure is generated using lattice device, the syntax is too
complicated for me: when I place the xlim=c(0,Y) in the arguments —
where Y is obtained using max(data) — there is no result. In basic R
this argument would work virtually in any position.
Any tip?
Best regards
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("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)
X<-c(0.7, 1.3, 1.7, 2.3)
Y<-max(copy)
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()
k<-0
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, ...)
}
}
)
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