Please, reproduce this code:
install.packages('lattice')
install.packages('zoo')
require(lattice)
require(zoo)
X <- matrix(runif(25 * 8), ncol = 8)
(Its purpose is just to load packages and to create a matrix with 8 columns).
Using zoo it is very easy to create such a plot:
plot.zoo(X, screen = c(1,1,2,2,3,3,4,4), col = c(1,2))
How can I make the same with lattice's xyplot() function?
This can be done via zoo:::xyplot.zoo: as reported in zoo package documentation, xyplot.zoo has xyplot methods for time series objects.
Then, for what concerns the above question, it is possible to use:
xyplot(as.zoo(X), screen = c(1,1,2,2,3,3,4,4), col = c(1,2))
to produce a trellis object like in lattice selecting the desired layout with the screen argument.
Related
My problem is multifaceted.
I would like to plot multiple columns saved in a data frame. Those columns do not have an x variable but would essentially be 1 to 101 consistent for all. I have seen that I can transfer them into long format but most ggplot options require an X. I tried zoo which does what I want it to, but the x-label is all jumbled and I am not aware of how to fix it. (Example of data below, and plot)
df <- zoo(HIP_131_Y0_LC_walk1[1:9])
plot(df)
I have multiple data frames saved in a list so ultimately would like to run a function and apply to all. The zoo function solves step one but I am not able to apply to all the data frames in the list.
graph<-lapply(myfiles,function(x) zoo(x) )
print(graph)
Ideally I would like to also mark minimum and maximum, which I am aware can be done with ggplot but not zoo.
Thank you so much for your help in advance
Assuming that the problem is overlapped panel names there are numerous solutions to this:
abbreviate the names using abbreviate. We show this for plot.zoo and autoplot.zoo .
put the panel name in the upper left. We show this for plot.zoo using a custom panel.
Use a header on each panel. We show this using xyplot.zoo and using ggplot.
The examples below use the test input in the Note at the end. (Next time please provide a complete example including all input in reproducible form.)
The first two examples below abbreviates the panel names and using plot.zoo and autoplot.zoo (which uses ggplot2). The third example uses xyplot.zoo (which uses lattice). This automatically uses headers and is probably the easiest solution.
library(zoo)
plot(z, ylab = abbreviate(names(z), 8))
library(ggplot2)
zz <- setNames(z, abbreviate(names(z), 8))
autoplot(zz)
library (lattice)
xyplot(z)
(click on plots to see expanded; continued after plots)
This fourth example puts the panel names in the upper left of the panel themselves using plot.zoo with a custom panel.
pnl <- function(x, y, ..., pf = parent.frame()) {
legend("topleft", names(z)[pf$panel.number], bty = "n", inset = -0.1)
lines(x, y)
}
plot(z, panel = pnl, ylab = "")
(click on plot to see it expanded)
We can also get headers with autoplot.zoo similar to in lattice above.
library(ggplot2)
autoplot(z, facets = ~ Series, col = I("black")) +
theme(legend.position = "none")
(click to expand; continued after graphics)
List
If you have a list of vectors L (see Note at end for a reproducible example of such a list) then this will produce a zoo object:
do.call("merge", lapply(L, zoo))
Note
Test input used above.
library(zoo)
set.seed(123)
nms <- paste0(head(state.name, 9), "XYZ") # long names
m <- matrix(rnorm(101*9), 101, dimnames = list(NULL, nms))
z <- zoo(m)
L <- split(m, col(m)) # test list using m in Note
I am trying to create and record plots in a 1x1 device:
par(mfrow = c(1, 1) )
plot(rnorm(10) )
p1 <- recordPlot()
plot(rnorm(20) )
p2 <- recordPlot()
and then to put them in a new layout (e.g., a 1x2 device):
par(mfrow = c(1, 2) )
p1
p2
However, this produce the same effect (i.e., plotting each plot in a 1x1 device). It seems replaying plots uses the original layout (graphical parameters) that was in effect when they were recorded.
Is there some method that allows a saved plot to be replayed in a new layout ?
NB: I am aware this would be easier via ggplot2, but my question is about base plots.
I did some digging, and I don't think this is possible. I used the following to look at what attributes are available inside the object. None of them seemed to indicate the layout could be adjusted.
summary(p1)
p1[[1]]
p1[[2]]
If you need the same plot across two different layouts could you use set.seed() to recreated the same plot? See the example below.
par(mfrow = c(1, 1))
set.seed(1234)
plot(rnorm(10))
par(mfrow = c(1, 2))
set.seed(1234)
plot(rnorm(10))
I'd be interested to see if anyone else has a better answer!
We can plot candle stick chart using chart series function chartSeries(Cl(PSEC)) I have created some custom values (I1,I2 and I3) which I want to plot together(overlay) outside the candle stick pattern. I have used addTA() for this purpose
chartSeries(Cl(PSEC)), TA="addTA(I1,col=2);addTA(I2,col=3);addTA(I3,col=4)")
The problem is that it plots four plots for Cl(PSEC),I1,I2 and I3 separately instead of two plots which I want Cl(PSEC) and (I1,I2,I3)
EDITED
For clarity I am giving a sample code with I1, I2 and I3 variable created for this purpose
library(quantmod)
PSEC=getSymbols("PSEC",auto.assign=F)
price=Cl(PSEC)
I1=SMA(price,3)
I2=SMA(price,10)
I3=SMA(price,15)
chartSeries(price, TA="addTA(I1,col=2);addTA(I2,col=3);addTA(I3,col=4)")
Here is an option which preserves largely your original code.
You can obtain the desired result using the option on=2 for each TA after the first:
library(quantmod)
getSymbols("PSEC")
price <- Cl(PSEC)
I1 <- SMA(price,3)
I2 <- SMA(price,10)
I3 <- SMA(price,15)
chartSeries(price, TA=list("addTA(I1, col=2)", "addTA(I2, col=4, on=2)",
"addTA(I3, col=5, on=2)"), subset = "last 6 months")
If you want to overlay the price and the SMAs in one chart, you can use the option on=1 for each TA.
Thanks to #hvollmeier who made me realize with his answer that I had misunderstood your question in the previous version of my answer.
PS: Note that several options are described in ?addSMA(), including with.col which can be used to select a specific column of the time series (Cl is the default column).
If I understand you correctly you want the 3 SMAs in a SUBPLOT and NOT in your main chart window.You can do the following using newTA.
Using your data:
PSEC=getSymbols("PSEC",auto.assign=F)
price=Cl(PSEC)
Now plotting a 10,30,50 day SMA in a window below the main window:
chartSeries(price['2016'])
newSMA <- newTA(SMA, Cl, on=NA)
newSMA(10)
newSMA(30,on=2)
newSMA(50,on=2)
The key is the argument on. Use on = NA in defining your new TA function, because the default value foron is 1, which is the main window. on = NA plots in a new window. Then plot the remaining SMAs to the same window as the first SMA. Style the colours etc.to your liking :-).
You may want to consider solving this task using plotting with the newer quantmod charts in the quantmod package (chart_Series as opposed to chartSeries).
Pros:
-The plots look cleaner and better (?)
-have more flexibility via editing the pars and themes options to chart_Series (see other examples here on SO for the basics of things you can do with pars and themes)
Cons:
-Not well documented.
PSEC=getSymbols("PSEC",auto.assign=F)
price=Cl(PSEC)
chart_Series(price, subset = '2016')
add_TA(SMA(price, 10))
add_TA(SMA(price, 30), on = 2, col = "green")
add_TA(SMA(price, 50), on = 2, col = "red")
# Make plot all at once (this approach is useful in shiny applications):
print(chart_Series(price, subset = '2016', TA = 'add_TA(SMA(price, 10), yaxis = list(0, 10));
add_TA(SMA(price, 30), on = 2, col = "purple"); add_TA(SMA(price, 50), on = 2, col = "red")'))
I'm working with some custom functions and I need to draw contours for them based on multiple values for the parameters.
Here is an example function:
I need to draw such a contour plot:
Any idea?
Thanks.
First you construct a function, fourvar that takes those four parameters as arguments. In this case you could have done it with 3 variables one of which was lambda_2 over lambda_1. Alpha1 is fixed at 2 so alpha_1/alpha_2 will vary over 0-10.
fourvar <- function(a1,a2,l1,l2){
a1* integrate( function(x) {(1-x)^(a1-1)*(1-x^(l2/l1) )^a2} , 0 , 1)$value }
The trick is to realize that the integrate function returns a list and you only want the 'value' part of that list so it can be Vectorize()-ed.
Second you construct a matrix using that function:
mat <- outer( seq(.01, 10, length=100),
seq(.01, 10, length=100),
Vectorize( function(x,y) fourvar(a1=2, x/2, l1=2, l2=y/2) ) )
Then the task of creating the plot with labels in those positions can only be done easily with lattice::contourplot. After doing a reasonable amount of searching it does appear that the solution to geom_contour labeling is still a work in progress in ggplot2. The only labeling strategy I found is in an external package. However, the 'directlabels' package's function directlabel does not seem to have sufficient control to spread the labels out correctly in this case. In other examples that I have seen, it does spread the labels around the plot area. I suppose I could look at the code, but since it depends on the 'proto'-package, it will probably be weirdly encapsulated so I haven't looked.
require(reshape2)
mmat <- melt(mat)
str(mmat) # to see the names in the melted matrix
g <- ggplot(mmat, aes(x=Var1, y=Var2, z=value) )
g <- g+stat_contour(aes(col = ..level..), breaks=seq(.1, .9, .1) )
g <- g + scale_colour_continuous(low = "#000000", high = "#000000") # make black
install.packages("directlabels", repos="http://r-forge.r-project.org", type="source")
require(directlabels)
direct.label(g)
Note that these are the index positions from the matrix rather than the ratios of parameters, but that should be pretty easy to fix.
This, on the other hand, is how easilyy one can construct it in lattice (and I think it looks "cleaner":
require(lattice)
contourplot(mat, at=seq(.1,.9,.1))
As I think the question is still relevant, there have been some developments in the contour plot labeling in the metR package. Adding to the previous example will give you nice contour labeling also with ggplot2
require(metR)
g + geom_text_contour(rotate = TRUE, nudge_x = 3, nudge_y = 5)
I have the following Problem. After running an ordered logit model, I want to R's effects package to visualize the results. This works fine and I did so for two independent variables, then I tried to combine the two plots. However, this does not seem to work. I provide a little replicable example here so you can see my problem for yourself:
library(car)
data(Chile)
mod <- polr(vote ~ age + log(income), data=Chile)
eff <- effect("log(income)", mod)
plot1 <- plot(eff, style="stacked",rug=F, key.args=list(space="right"))
eff2 <- effect("age", mod)
plot2 <- plot(eff2, style="stacked",rug=F, key.args=list(space="right"))
I can print these two plots now independently, but when I try to plot them together, the first plot is overwritten. I tried setting par(mfrow=c(2,1)), which didn't work. Next I tried the following:
print(plot1, position=c(0, .5, 1, 1), more=T)
print(plot2, position=c(0,0, 1, .5))
In this latter case, the positions of the two plots are just fine, but still the first plot vanishes once I add the second (or better, it is overwritten). Any suggestions how to prevent this behavior would be appreciated.
Reading down the long list of arguments to ?print.eff we see that there are some arguments for doing just this:
plot(eff, style="stacked",rug=F, key.args=list(space="right"),
row = 1,col = 1,nrow = 1,ncol = 2,more = TRUE)
plot(eff2, style="stacked",rug=F, key.args=list(space="right"),
row = 1,col = 2,nrow = 1,ncol = 2)
The reason par() didn't work is because this package is using lattice graphics, which are based on the grid system, which is incompatible with base graphics. Neither par() nor layout will have any effect on grid graphics.
This seems to work:
plot(eff,col=1,row=2,ncol=1,nrow=2,style="stacked",rug=F,
key.args=list(space="right"),more=T)
plot(eff2,col=1,row=1,ncol=1,nrow=2,style="stacked",rug=F,
key.args=list(space="right"))
edit: Too late...