Hi Anna
I got down to
plot2_3_concentration <-
xyplot(Value ~ Year, datamystuff23, groups = Type, ...
and got an error:
Error in eval(substitute(groups), data, environment(x)) :
object 'datamystuff23' not found
so I did not pursue further
Note : from ?doubleYScale
Note that most settings, like main/sub/legend/etc are taken only from obj1;
only the panel, axis and ylab are taken from obj2.
As we are now working with 2 plots you can reduce the complexity of your
plots and you may get away without having to use a panel function.
Try without a panel function and then a panel function. You may then get
away with a panel.xyplot in the panel without having to resort to
panel.groups.
Settings for the key are those found in the trellis.par.get()$superpose. ...
series ie. trellis.par.get()$superpose.line,
trellis.par.get()$superpose.symbol etc
You can setup par.settings adding
superpose.symbol = list(...),
superpose.line = list( ...)
or what I have done
key = list(text = list(label = c("stuff1","stuff2","stuff3")),
lines = list(col = 1:3),
cex = 0.8,
title = "stuff type",
cex.title = 0.9,
space = "bottom"),
col = c(1:3) # for points
)
and modify accordingly. I usually find it is easier to have a custom key as
I have to make changes to various parts of the key and it is easier to add
on things there.
Duncan
-----Original Message-----
From: Anna Zakrisson Braeunlich [mailto:anna.zakris...@su.se]
Sent: Sunday, 3 August 2014 15:10
To: Duncan Mackay
Subject: RE: [R] lattice, latticeExtra: Adding moving averages to double y
plot
Hi Duncan,
I think you have misunderstood my plot. I am able to change lty the way you
have plotted it with points on one axis and moving averages on the other. if
you run the code below, you find the plot that I need to do. data points and
moving averages for factor 1 on one yaxis (temperature) and factor 2 and 3
(data points and moving averages on the second y-axis: summer and winter
concentrations of compound X). See the plot below to better see what I mean.
1. My problem is to change lty for the axis where I have temperature. I
somehow need to specify that lty is depending on factor, which I am not able
to do. I have marked the position in plot2_3 where I have a problem.
2. The second issue is the symbols (pch). I have managed to change these in
the plot, but cannot make them appear in the legend. How would I go about
this? See comments in script.
Below is the full script with a correct plot with the issues at hand
labelled.
many thank's for your time!
Anna
############################################################################
#####
############################
mydata<- data.frame(
Year = 1980:2009,
Type = factor(rep(c("stuff1", "stuff2", "stuff3"), each = 10*3)),
Value = rnorm(90, mean = seq(90),
sd = rep(c(6, 7, 3), each = 10)))
# stuff1 is temperature
# stuff 2 and stuff 3 are concentration measurements of compound X
library(lattice)
library(latticeExtra)
stuff1data <- mydata[(mydata$Type) %in% c("stuff1"), ]
stuff2_3data <- mydata[(mydata$Type) %in% c("stuff2", "stuff3"), ]
# make moving averages function using zoo and rollmean:
library(zoo)
library(plyr)
f <- function(d)
{
require(zoo)
data.frame(Year = d$Year[5:length(d$Year)],
mavg = rollmean(d$Value, 5))
}
# Apply the function to each group as well as both data frames:
madfStuff1 <- ddply(stuff1data, "Type", f)
madfStuff2_3 <- ddply(stuff2_3data, "Type", f)
# combine averages into mydata
mydata$mavg <-
c(rep(NA,4), madfStuff1[,3],
rep(NA,4), subset(madfStuff2_3, Type== "stuff2",3, drop = T),
rep(NA,4), subset(madfStuff2_3, Type== "stuff3",3, drop = T))
table(mydata$Type)
# split stuff1 from stuff2/3 as they will read off different y-axes
stuff1mavg_points <- mydata[(mydata$Type) %in% c("stuff1"), ] #temperature
stuff23mavg_points <- mydata[(mydata$Type) %in% c("stuff2", "stuff3"), ] #
concentration
# plot stuff2/3 with data points and moving averages reading off y-axis 1:
plot2_3_concentration <- xyplot(Value ~ Year, datamystuff23, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
par.settings = list(layout.heights = list(key.top = 1.5)),
col = "black", pch=c(2,15),
ylab="concentration",
subscripts = TRUE,
panel = panel.superpose,
panel.groups = function(x, y, subscripts,
...,group.number) {
panel.xyplot(x, y, ...)
panel.xyplot(x, datamystuff23[subscripts,"mavg"], type =
"l", col="black",
lty = c(1:2)) # HERE IS THE PROBLEM!
LTY!!!
})
plot2_3_concentration
# If I use l lty = c(1:2)[group.number], I get only one line!
# plot stuff 1: with data points and moving averages reading off y-axis 2
plot1_temperature<- xyplot(Value ~ Year, datamystuff1, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
par.settings = list(layout.heights = list(key.top = 1.5)),
col = "black", pch=4,
subscripts = TRUE,
ylab="temperature",
panel = panel.superpose,
panel.groups = function(x, y, subscripts, ...,group.number) {
panel.xyplot(x, y, ...)
panel.xyplot(x, mydata[subscripts,"mavg"], col =
c(1:3)[group.number], type = "l", lty=3) #
HERE I AM ABLE TO MODIFY LTY
})
plot1_temperature
doubleYScale(plot2_3_concentration, plot1_temperature, style1 = 0, style2=0,
add.ylab2 = TRUE,
text = c("winter concentration cpd X", "summer concentration
cpd X",
"temperature"), lty=c(1:3), columns = 2,
col=c("black", "black", "black")) # HERE TWO LINES ARE FULLY
DRAWN!
update(trellis.last.object(),
par.settings = simpleTheme(col = c("black", "black"), lty=c(1:3),
pch=c(2,4,15))) # WHY CAN I NOT SEE PCH IN
THE LEGEND?
Anna Zakrisson Braeunlich
PhD student
Department of Ecology, Environment and Plant Sciences
Stockholm University
Svante Arrheniusv. 21A
SE-106 91 Stockholm
Sweden/Sverige
Lives in Berlin.
For paper mail:
Katzbachstr. 21
D-10965, Berlin
Germany/Deutschland
E-mail: anna.zakris...@su.se
Tel work: +49-(0)3091541281
Mobile: +49-(0)15777374888
LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
><((((º>`. . `. . `. . ><((((º>`. . `. . `. .><((((º>`. . `.
. `. .><((((º>
________________________________________
From: Duncan Mackay [dulca...@bigpond.com]
Sent: 01 August 2014 06:38
To: R; Anna Zakrisson Braeunlich
Subject: RE: [R] lattice, latticeExtra: Adding moving averages to double y
plot
Hi Anna
I forgot you had problems with lty
I have cleaned up the yright and put lty in
yright <-
xyplot(mavg ~ Year, mydata, groups = Type,
type = "l",
ylab = "mean",
lty = 1:3,
par.settings = list(layout.heights = list(key.top = 1.5)), #
separate key from bottom a bit more
col = c(1:3) )
I did not change for what you wanted on the right as far as labels etc is
concerned
Duncan
-----Original Message-----
From: Duncan Mackay [mailto:dulca...@bigpond.com]
Sent: Friday, 1 August 2014 12:03
To: R; 'Anna Zakrisson Braeunlich'
Subject: RE: [R] lattice, latticeExtra: Adding moving averages to double y
plot
Hi Anna
I have gone back to doubleYScale because I started following the wrong
section that I had before so it was quicker to do doubleYScale
You need to have 2 lattice objects and components are taken from each below
so use the function str on the three objects to see
library(lattice)
library(latticeExtra)
yleft <-
xyplot(Value ~ Year, mydata, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
par.settings = list(layout.heights = list(key.top = 1.5)),
key = list(text = list(label = c("stuff1","stuff2","stuff3")),
lines = list(col = 1:3),
cex = 0.8,
title = "stuff type",
cex.title = 0.9,
space = "bottom"),
col = c(1:3) # for points
)
yright <-
xyplot(mavg ~ Year, mydata, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
type = "l",
ylab = "mean",
par.settings = list(layout.heights = list(key.top = 1.5)), #
separate key from bottom a bit more
col = c(1:3) )
# colours both y axes so change with next command
yboth <-
doubleYScale(yleft, yright, add.ylab2 = TRUE)
yboth
# change y axes col to suit
update(trellis.last.object(), # left # right
par.settings = simpleTheme(col = c("black", "cyan")))
Duncan
-----Original Message-----
From: Anna Zakrisson Braeunlich [mailto:anna.zakris...@su.se]
Sent: Friday, 1 August 2014 03:11
To: Duncan Mackay
Subject: RE: [R] lattice, latticeExtra: Adding moving averages to double y
plot
Hi Duncan,
Now I have found a solution to my problem. It is complete except for one
tiny detail: I am unable to define different line types for stuff2 and
stuff3 moving averages (see plot2_3).
mydata<- data.frame(
Year = 1980:2009,
Type = factor(rep(c("stuff1", "stuff2", "stuff3"), each = 10*3)),
Value = rnorm(90, mean = seq(90),
sd = rep(c(6, 7, 3), each = 10)))
library(lattice)
library(latticeExtra)
stuff1data <- mydata[(mydata$Type) %in% c("stuff1"), ]
stuff2_3data <- mydata[(mydata$Type) %in% c("stuff2", "stuff3"), ]
# make moving averages function using zoo and rollmean:
library(zoo)
library(plyr)
f <- function(d)
{
require(zoo)
data.frame(Year = d$Year[5:length(d$Year)],
mavg = rollmean(d$Value, 5))
}
# Apply the function to each group as well as both data frames:
madfStuff1 <- ddply(stuff1data, "Type", f)
madfStuff2_3 <- ddply(stuff2_3data, "Type", f)
# combine averages into mydata
mydata$mavg <-
c(rep(NA,4), madfStuff1[,3], # what is rep(NA,4) doing?
rep(NA,4), subset(madfStuff2_3, Type== "stuff2",3, drop = T), # is "3"
referring to the number of factors?
rep(NA,4), subset(madfStuff2_3, Type== "stuff3",3, drop = T))
table(mydata$Type)
# split stuff1 from stuff2/3
datamystuff1 <- mydata[(mydata$Type) %in% c("stuff1"), ]
datamystuff23 <- mydata[(mydata$Type) %in% c("stuff2", "stuff3"), ]
table(datamystuff23$Type)
xyplot(Value ~ Year, datamystuff23, groups=Type)
xyplot(mavg ~ Year, datamystuff23, groups=Type)
# plot stuff2/3:
plot2_3 <- xyplot(Value ~ Year, datamystuff23, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
par.settings = list(layout.heights = list(key.top = 1.5)),
col = "black", pch=c(2:3),
ylab="concentration",
subscripts = TRUE,
panel = panel.superpose,
panel.groups = function(x, y, subscripts,
...,group.number) {
panel.xyplot(x, y, ...)
panel.xyplot(x, datamystuff23[subscripts,"mavg"], col =
"black", type = "l", lty=c(1:2)) ### Why
can I not define different lty?
})
plot2_3 # plot is incorrect!
plot1<- xyplot(Value ~ Year, datamystuff1, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
par.settings = list(layout.heights = list(key.top = 1.5)),
col = "black", pch=c(2:3),
subscripts = TRUE,
ylab="temperature",
panel = panel.superpose,
panel.groups = function(x, y, subscripts, ...,group.number) {
panel.xyplot(x, y, ...)
panel.xyplot(x, mydata[subscripts,"mavg"], col =
c(1:3)[group.number], type = "l", lty=3)
})
plot1 # this plot looks correct!
doubleYScale(plot2_3, plot1, style1 = 0, style2=0, add.ylab2 = TRUE,
text = c("nitrogen", "winter temperature", "summer
tempareture"), lty=c(1:3),columns = 2,
col=c("black", "black", "black"))
update(trellis.last.object(),
par.settings = simpleTheme(col = c("black", "black"),
lty=c(1:3),
pch=c(1:3)))
Anna Zakrisson Braeunlich
PhD student
Department of Ecology, Environment and Plant Sciences
Stockholm University
Svante Arrheniusv. 21A
SE-106 91 Stockholm
Sweden/Sverige
Lives in Berlin.
For paper mail:
Katzbachstr. 21
D-10965, Berlin
Germany/Deutschland
E-mail: anna.zakris...@su.se
Tel work: +49-(0)3091541281
Mobile: +49-(0)15777374888
LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
><((((º>`. . `. . `. . ><((((º>`. . `. . `. .><((((º>`. . `.
. `. .><((((º>
________________________________________
From: Duncan Mackay [dulca...@bigpond.com]
Sent: 31 July 2014 06:17
To: R; Anna Zakrisson Braeunlich
Subject: RE: [R] lattice, latticeExtra: Adding moving averages to double y
plot
Hi Anna
I am still unsure what you want
1 do you want 1 panel or 3?
2 do you want 1 y axis on the left and 1 on the right
or 1 y axis on the left and 2 on the right
or 1 on the right varying with
groups in a multipanel plot
For starters try
xyplot(Value ~ Year, mydata, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
par.settings = list(layout.heights = list(key.top = 1.5)), #
separate key from bottom a bit more
col = c("black","black","black"), # for points
key = list(text = list(label = c("stuff1","stuff2","stuff3")),
lines = list(col = 1:3),
cex = 0.8,
title = "stuff type",
cex.title = 0.9,
space = "bottom"),
subscripts = TRUE,
panel = panel.superpose,
panel.groups = function(x, y, subscripts, ...,group.number) {
panel.xyplot(x, y, ...)
panel.xyplot(x, mydata[subscripts,"mavg"], col =
c(1:3)[group.number], type = "l")
})
OR
xyplot(Value ~ Year|Type, mydata,
allow.multiple = T,
aspect = 0.75,
layout = c(1,3),
groups = Type,
distribute.type = TRUE,
par.settings = list(layout.heights = list(key.top = 1.5)), #
separate key from bottom a bit more
scales = list(alternating = F),
col = c("black","black","black"),
subscripts = TRUE,
key = list(text = list(label = c("stuff1","stuff2","stuff3")),
lines = list(col = 1:3),
cex = 0.8,
title = "stuff type",
cex.title = 0.9,
space = "bottom"),
panel = panel.superpose,
panel.groups = function(x, y, subscripts, ...,group.number) {
panel.xyplot(x, y, ...)
panel.xyplot(x, mydata[subscripts,"mavg"], col =
c(1:3)[group.number], type = "l")
})
have a look at
?lattice::axis.default
for yscale.components
This means that you only need 1 xyplot object
if you use doubleYScale you need to xyplot objects
1 for the points and another for the averages
These are then superimposed with the doubleYScale
Also read and re read ?xyplot
names(trellis.par.get()) give you a list of the names in trellis.par.get()
and trellis.par.get() gives you all the settings used by argument
par.settings in xyplot and those in the lattice series
par.settings may help you with themes.
http://lmdvr.r-forge.r-project.org/figures/figures.html
may be instructive
Duncan
-----Original Message-----
From: Anna Zakrisson Braeunlich [mailto:anna.zakris...@su.se]
Sent: Wednesday, 30 July 2014 23:59
To: Duncan Mackay
Subject: RE: [R] lattice, latticeExtra: Adding moving averages to double y
plot
Hi Duncan and many thank's for your help!
I could see your first message perfectly.
You solved my problem to some extent. What my problem is, is that I need a
double y plot with two of these moving averages belonging to one axis (both
are temperature measurements, say Stuff 2 and 3, measured in degrees C) the
other one reading off the second axis (a nutrient measurement in mM (say
Stuff1)).
How can I plot Stuff2 and stuff3 moving averages in one plot and stuff1 in
another and then combine them using doubleYscale?
I also have some other annotated questions regarding linetypes. I could
change symbols using pch, but not the line type. Why? See code below:
Many many thank's once again.
mydata<- data.frame(
Year = 1980:2009,
Type = factor(rep(c("stuff1", "stuff2", "stuff3"), each = 10*3)),
Value = rnorm(90, mean = seq(90),
sd = rep(c(6, 7, 3), each = 10)))
library(lattice)
library(latticeExtra)
stuff1data <- mydata[(mydata$Type) %in% c("stuff1"), ]
stuff2_3data <- mydata[(mydata$Type) %in% c("stuff2", "stuff3"), ]
# make moving averages function using zoo and rollmean:
library(zoo)
library(plyr)
f <- function(d)
{
require(zoo)
data.frame(Year = d$Year[5:length(d$Year)],
mavg = rollmean(d$Value, 5))
}
# Apply the function to each group as well as both data frames:
madfStuff1 <- ddply(stuff1data, "Type", f)
madfStuff2_3 <- ddply(stuff2_3data, "Type", f)
# Some styles:
myStripStyle <- function(which.panel, factor.levels, ...) {
panel.rect(0, 0, 1, 1,
col = bgColors[which.panel],
border = 1)
panel.text(x = 0.5, y = 0.5,
font=2,
lab = factor.levels[which.panel],
col = txtColors[which.panel])
}
mydata$mavg <-
c(rep(NA,4), madfStuff1[,3], # what is rep(NA,4) doing?
rep(NA,4), subset(madfStuff2_3, Type== "stuff2",3, drop = T), # is "3"
referring to the number of factors?
rep(NA,4), subset(madfStuff2_3, Type== "stuff3",3, drop = T))
xyplot(Value ~ Year, mydata, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
col = c("black","black","black"),
subscripts = TRUE,
par.settings = simpleTheme(lty=c(1:3), pch=c(1:3)), #why can I change
symbol (pch), but not line type (lty)?
panel = panel.superpose,
panel.groups = function(x, y, subscripts, ...,group.number) {
panel.xyplot(x, y, ...)
panel.xyplot(x, mydata[subscripts,"mavg"], col =
c("black","black","black")[group.number], type =
"l") # tried to change lty here too lty=c(1:3), but # without success
})
# how can I add a legend specifying the linetype AS WELL AS symbol?
# I tried using: text = c("stuff1", "stuff2", "stuff3"), columns = 2 but
could not make it work.
Anna Zakrisson Braeunlich
PhD student
Department of Ecology, Environment and Plant Sciences
Stockholm University
Svante Arrheniusv. 21A
SE-106 91 Stockholm
Sweden/Sverige
Lives in Berlin.
For paper mail:
Katzbachstr. 21
D-10965, Berlin
Germany/Deutschland
E-mail: anna.zakris...@su.se
Tel work: +49-(0)3091541281
Mobile: +49-(0)15777374888
LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
><((((º>`. . `. . `. . ><((((º>`. . `. . `. .><((((º>`. . `.
. `. .><((((º>
________________________________________
From: Duncan Mackay [dulca...@bigpond.com]
Sent: 29 July 2014 01:45
To: R; Anna Zakrisson Braeunlich
Subject: RE: [R] lattice, latticeExtra: Adding moving averages to double y
plot
I do not know what happened to my last email as this are set up as plain
text so I am sending the code again so I hope this works
I am not sure what you wanted exactly but this will plot the points and
lines of the average.
I have not worried about the 2nd axis
Here is one way of doing things by combining the averages into the
dataframe.
It makes it easier that way as you do not have to match up the x values
# combine averages into mydata
mydata$mavg <-
c(rep(NA,4), madfStuff1[,3],
rep(NA,4), subset(madfStuff2_3, Type== "stuff2",3, drop = T),
rep(NA,4), subset(madfStuff2_3, Type== "stuff3",3, drop = T))
xyplot(Value ~ Year, mydata, groups = Type,
allow.multiple = T,
distribute.type = TRUE,
col = c("red","blue","cyan"),
subscripts = TRUE,
panel = panel.superpose,
panel.groups = function(x, y, subscripts, ...,group.number) {
panel.xyplot(x, y, ...)
panel.xyplot(x, mydata[subscripts,"mavg"], col =
c("red","blue","cyan")[group.number], type = "l")
})
Duncan
BTW libraries are case sensitive as well. Is it you editor putting capitals?
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mac...@northnet.com.au
-----Original Message-----
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Anna Zakrisson Braeunlich
Sent: Monday, 28 July 2014 16:38
To: r-help@r-project.org
Subject: [R] lattice, latticeExtra: Adding moving averages to double y plot
Hi lattice users,
I would like to add 5-year moving averages to my double y-plot. I have three
factors needs to be plotted with moving averages in the same plot. One of
these reads off y-axis 1 and two from y-axis 2. I have tried to use the
rollmean function from the zoo-packages, but I fail in insering this into
lattice (I am not an experienced lattice user). I want to keep the data
points in the plot.
Find below dummy data and the script as well as annotations further
describing my question.
thank you in advance!
Anna Zakrisson
mydata<- data.frame(
Year = 1980:2009,
Type = factor(rep(c("stuff1", "stuff2", "stuff3"), each = 10*3)),
Value = rnorm(90, mean = seq(90),
sd = rep(c(6, 7, 3), each = 10)))
library(Lattice)
library(LatticeExtra)
stuff1data <- mydata[(mydata$Type) %in% c("stuff1"), ]
stuff12_3data <- mydata[(mydata$Type) %in% c("stuff2", "stuff3"), ]
# make moving averages function using zoo and rollmean:
library(zoo)
library(plyr)
f <- function(d)
{
require(zoo)
data.frame(Year = d$Year[5:length(d$Year)],
mavg = rollmean(d$Value, 5))
}
# Apply the function to each group as well as both data frames:
madfStuff1 <- ddply(stuff1data, "Type", f)
madfStuff2_3 <- ddply(stuff12_3data, "Type", f)
# Some styles:
myStripStyle <- function(which.panel, factor.levels, ...) {
panel.rect(0, 0, 1, 1,
col = bgColors[which.panel],
border = 1)
panel.text(x = 0.5, y = 0.5,
font=2,
lab = factor.levels[which.panel],
col = txtColors[which.panel])
}
myplot1 <- xyplot(Value ~ Year, data = stuff1data, col="black",
lty=1, pch=1,
ylab = "sweets", strip.left = F,
strip=myStripStyle,
xlab = ("Year"),
panel = function(x,y,...,subscripts){
panel.xyplot(x, y, pch = 1,col = "black")
panel.lmline(x,y,col = "black", data=madfStuff1) # here
I presume that panel.lmline is wrong.
# I would like to have my 5 year moving average here,
not a straight line.
})
myplot1
myplot2 <- xyplot(Value ~ Year, data = stuff12_3data, col="black",
lty=1, pch=1,
ylab = "hours", strip.left = F,
strip=myStripStyle,
xlab = ("Year"),
panel = function(x,y,...,subscripts){
panel.xyplot(x, y, pch = c(2:3),col = "black") ## what
is this "pch" defining? Types?
#I would like to have different symbols and line types
for stuff2 and stuff3
panel.lmline(x,y,col = "black", data=madfStuff2_3) #
wrong! Need my moving averages here!
})
myplot2
doubleYScale(myplot1, myplot2, style1 = 0, style2=0, add.ylab2 = TRUE,
text = c("stuff1", "stuff2", "stuff3"), columns = 2,
col="black")
# problem here is that I end up with two lines. I need a double y-plot with
one moving average plots that are read off y-axis 1
# and two that reads off y-axis 2. I need to keep the data points in the
plot.
update(trellis.last.object(),
par.settings = simpleTheme(col = c("black", "black"), lty=c(1:3),
pch=c(1:3))) # how come that I only get
# lines in my legend text and not the symbols too. I thought "pch" would add
symbols?!?
Anna Zakrisson Braeunlich
PhD student
Department of Ecology, Environment and Plant Sciences
Stockholm University
Svante Arrheniusv. 21A
SE-106 91 Stockholm
Sweden/Sverige
Lives in Berlin.
For paper mail:
Katzbachstr. 21
D-10965, Berlin
Germany/Deutschland
E-mail: anna.zakris...@su.se
Tel work: +49-(0)3091541281
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