I'd like to plot something like this:
plot(dnorm(mean=2),from=-3,to=3)
But it doesn't work as if you do:
plot(dnorm,from=-3,to=3)
what is the problem?
The answer you received from #r2evans is excellent. You might also want to consider learning ggplot, as in the long run it will likely make your life much easier. In that case, you can use stat_function which will plot the results of an arbitrary function along a grid of the x variable. It accepts arguments to the function as a list.
library(ggplot2)
ggplot(data = data.frame(x=c(-3,3)), aes(x = x)) +
stat_function(fun = dnorm, args = list(mean = 2))
curve(dnorm(x, mean = 2), from = -3, to = 3)
The curve function looks for the xname= variable (defaults to x) in the function call, so in dnorm(x, mean=2), it is not referencing an x in the calling environment, it is a placeholder for curve to use for iterated values.
The reason plot(dnorm, ...) works as it does is because there exists graphics::plot.function, since dnorm in that case is a function. When you try plot(dnorm(mean=2)), the dnorm(mean=2) is no longer a function, it is a call ... that happens to fail because it requires x (its first argument) be provided.
Incidentally, plot.function calls curve(...), so other than being a convenience function, there is very little reason to use plot(dnorm, ...) over curve(dnorm(x), ...) other than perhaps a little code-golf. The biggest advantage to curve is that it lets you control arbitrary arguments to the dnorm() function, whereas plot.function does not.
Related
I am currently trying to plot some density distributions functions with R's ggplot2. I have the following code:
f <- stat_function(fun="dweibull",
args=list("shape"=1),
"x" = c(0,10))
stat_F <- stat_function(fun="pweibull",
args=list("shape"=1),
"x" = c(0,10))
S <- function() 1 - stat_F
h <- function() f / S
wei_h <- ggplot(data.frame(x=c(0,10))) +
stat_function(fun=h) +
...
Basically I want to plot hazard functions based on a Weibull Distribution with varying parameters, meaning I want to plot:
The above code gives me this error:
Computation failed in stat_function():
unused argument (x_trans)
I also tried to directly use
S <- 1 - stat_function(fun="pweibull", ...)
instead of above "workaround" with the custom function construction. This threw another error, since I was trying to do numeric arithmetics on an object:
non-numeric argument for binary operator
I get that error, but I have no idea for a solution.
I have done some research, but without success. I feel like this should be straightforward. Also I would like to do it "manually" as much as possible, but if there is no simple way to do this, then a packaged solution is just fine aswell.
Thanks in advance for any suggestions!
PS: I basically want to recreate the graph you can find in Kiefer, 1988 on page 10 of the linked PDF file.
Three comments:
stat_function is a function statistic for ggplot2, you cannot divide two stat_function expressions by each other or otherwise use them in mathematical expressions, as in S <- 1 - stat_function(fun="pweibull", ...). That's a fundamental misunderstanding of what stat_function is. stat_function always needs to be added to a ggplot2 plot, as in the example below.
The fun argument for stat_function takes a function as an argument, not a string. You can define functions on the fly if you need ones that don't exist already.
You need to set up an aesthetic mapping, via the aes function.
This code works:
args = list("shape" = 1.2)
ggplot(data.frame(x = seq(0, 10, length.out = 100)), aes(x)) +
stat_function(fun = dweibull, args = args, color = "red") +
stat_function(fun = function(...){1-pweibull(...)}, args = args, color = "green") +
stat_function(fun = function(...){dweibull(...)/(1-pweibull(...))},
args = args, color = "blue")
My objective is pass lists as arguments to the function geom_point2 using lapply or analogously mapply. In similar situations, I had success passing a list (or lists) to geom_cladelabel as in:
mapply(function (x,y,z,w,v,u,t,s) geom_cladelabel(node=x, label=y,
align=F, etc. # Where x y z etc are lists.
Problem is related to the use of aes inside geom_point2. (not in geom_cladelabel):
In the case of geom_point2, the node info is inside aes, and I could't do it. Normally I do not get any error message, but it does not work.
The objective is to make this example work, but using mapply instead of writting geom_point2 two times.
# source("https://bioconductor.org/biocLite.R")
# biocLite("ggtree")
library(ggtree)
library(ape)
#standard code
newstree<-rtree(10)
node1<-getMRCA(newstree,c(1,2))
node2<-getMRCA(newstree,c(3,4))
ggtree(newstree)+
geom_point2(aes(subset=(node ==node1) ), fill="black", size=3, shape=23)+
geom_point2(aes(subset=(node ==node2) ), fill="green", size=3, shape=23)
#desire to substitute the geom_point2 layers with mapply or lapply:
#lapply(c(node1,node2), function (x) geom_point2(aes(subset=(node=x)))))
Here is a solution calling geom_point2 usig mapply:
library(ggtree)
ggtree(rtree(10)) +
mapply(function(x, y, z)
geom_point2(
aes_string(subset=paste("node ==", x)),
fill=y,
size=10,
shape=z
),
x=c(11,12),
y=c("green", "firebrick"),
z=c(23,24)
) +
geom_text2(aes(subset=!isTip, label=node))
The solution is in the aes_string(), which writes the value of x directly in the aesthetics. The default aes() does not pass on the value of x, but just the string "x". When plotting, ggtree then looks for a node called "x", and ends with an empty node list.
I guess this has to do with the variable being stored in the mapply-environment and not being passed on to the plot.
PS: Sorry for my too quick answer with do.call() earlier. It is useful, but off-topic here.
I understand how to use ellipses when I only want one function to receive those arguments:
ok <- function(x, ...){
sum(x, ...)
}
x.in <- c(1:9, NA)
ok(x.in, na.rm=TRUE)
I start getting confused when some functions need only certain parts of .... I was thinking of using something like names(formals(cor)) to test for which arguments in ... to send where, but I don't see how to do this for sum or plot. In general, I want to write functions similar to the following:
yikes <- function(x, ...){
plot(x, ...)
sum(x, ...) + cor(x, ...)
}
x.in <- c(1:9, NA)
x.in.jitter <- jitter(x.in)
yikes(x.in, y=x.in.jitter, na.rm=TRUE, use="na.or.complete", type="o")
Ideally, yikes() would do the following:
plot(x=x.in, y=x.in.jitter, type="o")
sum(x.in, na.rm=TRUE) + cor(x=x.in, y=x.in.jitter, use="na.or.complete")
I suspect part of the solution may use match.call. How would I get a function like yikes() to work? Is this simply a bad idea?
Edit: The second link in the first comment goes a long way to answering this question given the situation where you know/ are willing to explicitly describe what parameters get passed to what functions. Using the arguments of functions called directly (e.g., cor, plot, sum in yikes), or indirectly (par via plot) to indicate what arguments supplied via ... should be used for a particular function is what I am searching for. I understand the case for cor, e.g.; but how would one do this for plot, without explicitly mentioning par or the arguments it takes?
I have a family of functions that are all the same except for one adjustable parameter, and I want to plot all these functions on one set of axes all superimposed on one another. For instance, this could be sin(n*x), with various values of n, say 1:30, and I don't want to have to type out each command individually -- I figure there should be some way to do it programatically.
library(ggplot2)
define trig functions as a function of frequency: sin(x), sin(2x), sin(3x) etc.
trigf <- function(i)(function(x)(sin(i*x)))
Superimpose two function plots -- this works manually of course
ggplot(data.frame(x=c(0,pi)), aes(x)) + stat_function(fun=trigf(1)) + stat_function(fun=trigf(2))
now try to generalize -- my idea was to make a list of the stat_functions using lapply
plotTrigf <- lapply(1:5, function(i)(stat_function(fun=function(x)(sin(i*x))) ))
try using the elements of the list manually but it doesn't really work -- only the i=5 plot is shown and I'm not sure why when that's not what I referenced
ggplot(data.frame(x=c(0,pi)), aes(x)) +plotTrigf[[1]] + plotTrigf[[2]]
I Thought this Reduce might handle the 'generalized sum' to add to a ggplot() but it doesn't work -- it complains of a non-numeric argument to binary operator
Reduce("+", plotTrigf)
So I'm kind of stuck both in executing this strategy, or perhaps there's some other way to do this.
Are you using version R <3.2? The problem is that you actually need to evaluate your i parameter in your lapply call. Right now it's being left as a promise and not getting evaulated till you try to plot and at that point i has the last value it had in the lapply loop which is 5. Use:
plotTrigf <- lapply(1:5, function(i) {force(i);stat_function(fun=function(x)(sin(i*x))) })
You can't just add stat_function calls together, even without Reduce() you get the error
stat_function(fun=sin) + stat_function(fun=cos)
# Error in stat_function(fun = sin) + stat_function(fun = cos) :
# non-numeric argument to binary operator
You need to add them to a ggplot object. You can do this with Reduce() if you just specify the init= parameter
Reduce("+", plotTrigf, ggplot(data.frame(x=c(0,pi)), aes(x)))
And actually the special + operator for ggplot objects allows you to add a list of objects so you don't even need the Reduce at all (see code for ggplot2:::add_ggplot)
ggplot(data.frame(x=c(0,pi)), aes(x)) + plotTrigf
The final result is
You need to use force in order to make sure the parameter is being evaluated at the right time. It's a very useful technique and a common source of confusion in loops, you should read about it in Hadley's book http://adv-r.had.co.nz/Functions.html
To solve your question: you just need to add force(i) when defining all the plots, inside the lapply function, before making the call to stat_function. Then you can use Reduce or any other method to combine them. Here's a way to combine the plots using lapply (note that I'm using the <<- operator which is discouraged)
p <- ggplot(data.frame(x=c(0,pi)), aes(x))
lapply(plotTrigf, function(x) {
p <<- p + x
return()
})
I tried GGally package a little bit. Especially the ggpairs function. However, I cannot figure out how to use loess instead of lm when plot smooth. Any ideas?
Here is my code:
require(GGally)
diamonds.samp <- diamonds[sample(1:dim(diamonds)[1],200),]
ggpairs(diamonds.samp[,c(1,5)],
lower = list(continuous = "smooth"),
params = c(method = "loess"),
axisLabels = "show")
Thanks!
P.S. compare with the plotmatrix function, ggpairs is much much slower... As a result, most of the time, I just use plotmatrix from ggplot2.
Often it is best to write your own function for it to use. Adapted from this answer to similar question.
library(GGally)
diamonds_sample = diamonds[sample(1:dim(diamonds)[1],200),]
# Function to return points and geom_smooth
# allow for the method to be changed
custom_function = function(data, mapping, method = "loess", ...){
p = ggplot(data = data, mapping = mapping) +
geom_point() +
geom_smooth(method=method, ...)
p
}
# test it
ggpairs(diamonds_sample,
lower = list(continuous = custom_function)
)
Produces this:
Well the documentation doesn't say, so use the source, Luke
You can dig deeper into the source with:
ls('package:GGally')
GGally::ggpairs
... and browse every function it references ...
seems like the args get mapped into ggpairsPlots and then -> plotMatrix which then gets called
So apparently selecting smoother is not explicitly supported, you can only select continuous = "smooth". If it behaves like ggplot2:geom_smooth it internally automatically figures out which of the supported smoothers to call (loess for <1000 datapoints, gam for >=1000).
You might like to step it through the debugger to see what's happening inside your plot. I tried to follow the source but my eyes glaze over.
or 2. Browse on https://github.com/ggobi/ggally/blob/master/R/ggpairs.r [4/14/2013]
#' upper and lower are lists that may contain the variables 'continuous',
#' 'combo' and 'discrete'. Each element of the list is a string implementing
#' the following options: continuous = exactly one of ('points', 'smooth',
#' 'density', 'cor', 'blank') , ...
#'
#' diag is a list that may only contain the variables 'continuous' and 'discrete'.
#' Each element of the diag list is a string implmenting the following options:
#' continuous = exactly one of ('density', 'bar', 'blank');