I'm a relative beginner in R so please forgive me if it's a noob question.
So, is there a package which provides an easy interface to plot (real-real, mathematical) functions? I need coordinate axis with arrows (and their intersection should be (0;0)) and ticks, grid, etc. I want similar plots as in this document.
Background: now I create function plots with LaTeX's tikzpicture and axis but I'm using R to generate randomized exams since few months (R creates tex-files and include them into document) and would be nice if R can create similar plots (png, jpg), because axis in LaTeX is very slow.
Thanks!
I made you a little function for this
math_plot <- function(f, xlim = c(-2,2), ylim = c(-2,2),
xlab = "x", ylab = "f(x)", ax.ext = .02,
frame.plot = F, grid.tick = .1, ...){
curve(f, from = xlim[1], to = xlim[2], ylim = ylim,
axes = F, xlab = "", ylab = "",
frame.plot = frame.plot, ...)
# x-axis
axis(1, pos = 0)
arrows(x0 = xlim[2], x1 = xlim[2] + diff(xlim)*ax.ext, y0 = 0, length = .1)
mtext(text = xlab, side = 4, line = 0, las = 2, at = 0)
# y-axis
axis(2, pos = 0, las = 2)
arrows(y0 = ylim[2], y1 = ylim[2] + diff(ylim)*ax.ext, x0 = 0, length = .1)
mtext(text = ylab, side = 3, line = 0, at = 0)
grid(nx = diff(xlim)/grid.tick, ny = diff(ylim)/grid.tick)
}
# give it a function
math_plot(function(x) 3*x + 2 - 2*x^2, ylim = c(-2,4))
With R graphic tools such as arrows, points, abline, etc. you can draw practically anything.
Example
op <- par(mar=c(1, 1, 1, 1)) ## adjust outer margins
plot(x, y, type="n", axes=F, asp=1, xlab="", ylab="") ## asp=1 to maintain 1:1 aspect ratio
lines(x, y, lwd=2)
arrows(par()$usr[1], 0, par()$usr[2], length=.05) ## par()$usr helps to find xlim and ylim
arrows(0, par()$usr[3], 0, par()$usr[4], length=.05)
points((-5:5)*10, rep(0, 11), pch=3, cex=.6) ## pch=3 for crosses
points(rep(0, 11), (-5:5)*10, pch=3, cex=.6)
mtext("y", 3, -1, adj=.55, font=8)
mtext("x", 4, -1, padj=-1, las=2, font=8)
abline(h=(-5:5)*10, lty=3, col="gray")
abline(v=(-5:5)*10, lty=3, col="gray")
text(10, -4, "10", font=7, cex=.8)
text(-4, 10, "10", font=7, cex=.8)
par(op) ## reset par
Data
x <- (-10):10; y <- x^2 - 50
Related
I am trying to plot the trajectory of the ODE in R but I am getting this weird error. I am able to plot the nullclines of the phase plane but I am not able to plot the trajectory of the system. (In my case, the parameters are a and b, but I'm not sure what to do with the function call parameters here. This is from the default function I was given. Should I remove it in the function call?)
PeriodicSystem <- function(t, y, parameters) {
a <- a
b <- b
dx <- -x + (a*y) + ((x^2)*y)
dy <- b - (a*y) + ((x^2)*y)
list(c(dx,dy))
}
example4_flowField <- flowField(PeriodicSystem,
xlim = c(-0.01, .425),
ylim = c(0, .5),
add = FALSE,
ylab = TeX("$y$"),
xlab= TeX("$x$"),
frac=1,
add.legend=FALSE)
grid()
example4_nullclines <- nullclines(PeriodicSystem,
xlim = c(-0.01, .425),
ylim = c(0, .5),
lty = 2, lwd = 2,
col=c("lightseagreen","aquamarine4"),
add.legend=FALSE)
example4_flowField <- flowField(PeriodicSystem,
xlim = c(-0.01, .425),
ylim = c(0, .5),
add = FALSE,
ylab = TeX("$y$"),
xlab= TeX("$x$"),
frac=1,
add.legend=FALSE)
grid()
example4_nullclines <- nullclines(PeriodicSystem,
xlim = c(-0.01, .425),
ylim = c(0, .5),
lty = 2, lwd = 2,
col=c("lightseagreen","aquamarine4"),
add.legend=FALSE)
y0 <- matrix(c(0.1,0.3,
0,0,
0.1,0.2), 3, 2, byrow = TRUE)
example4_trajectory <- trajectory(PeriodicSystem,
y0 = y0,
pch=16,
tlim = c(0, 100),
col="black",
add=T, ylab=TeX("$x, y$"), xlab=TeX("$t$"))
grid()
Note: col has been reset as required
Error in checkFuncEuler(Func, times, y, parms, rho, Nstates) :
The number of derivatives returned by func() (1000must equal the length of the initial conditions vector (2)
I would like to plot two sets of values (from different datasets but for the same countries) with two x axes for several countries in two loops using par(new=T). R however overlays the second set of data starting from the last country.
Here you can see the result
https://www.dropbox.com/s/9x0dn7oom5czpwm/Rplot02.jpg?dl=0
Here is my code as an example for 2 countries only (I have 28).
par(mfrow=c(2,2))
par(mar = c(5,5,5,5), cex.axis=1)
for (i in colnames(DPreachdifft[,2:3])) {
plot(DPreachdifft$Diff, DPreachdifft[[i]],
type="p",col="red", xaxt="n", yaxt="n",
ylim = range(c(-25, 25)),
xlim = rev(range(DPreachdifft$Diff)),
ylab="delay(+) or advance(-) in years", xlab=NA, pch=16,
main = i, adj=0)
axis(side = 1, at=ticks,labels=ticks)
axis(side = 2)
abline(h=0)
}
par(new=T)
for (i in colnames(NPreachdifft[,2:3])) {
plot(NPreachdifft$Diff1, NPreachdifft[[i]],
type="p",col="blue", xaxt="n", yaxt="n",
ylim = range(c(-40, 40)),
xlab=NA, ylab=NA, pch=16)
axis(side = 3, at=ticks1)
mtext(side = 1, text="difference in DP", line = 2, adj = 0.5)
mtext(side = 3, text="difference in NP", line = 2, adj = 0.5)
}
I have plotted five graphs and a legend. The graphs work just fine, however the legens disappears without an error.
My preview in RStudio looks like this
When I zoom in, the area where the legend should be is blank.
I use the following code:
opar <- par (no.readonly = TRUE)
par (mfrow = c(3, 2))
library(deSolve)
# Plot A
LotVmod <- function (Time, State, Pars) {
with(as.list(c(State, Pars)), {
dx = (b*x) - (b*x*x/K) - (y*(x^k/(x^k+C^k)*(l*x/(1+l*h*x))))
dy = (y*e*(x^k/(x^k+C^k)*(l*x/(1+l*h*x)))) - (m*y)
return(list(c(dx, dy)))
})
}
Pars <- c(b = 1.080, e = 2.200, K = 130.000, k = 20.000, l = 2.000,
h = 0.030, C = 2.900, m = 0.050)
State <- c(x = 0.25, y = 2.75)
Time <- seq(1, 9, by = 1)
out <- as.data.frame(ode(func = LotVmod, y = State, parms = Pars, times = Time))
matplot(out[,-1], type = "l", xlim = c(1, 9), ylim = c(0, 45),
xlab = "time",
ylab = "population",
main = "Compartment A")
mtext ( "Coefficient of Variance 4.96", cex = 0.8 )
x <- c(# Validation data)
y <- c(# Validation data)
lines (Time, x, type="l", lty=1, lwd=2.5, col="black")
lines (Time, y, type="l", lty=1, lwd=2.5, col="red")
# Legend
plot.new()
legend("center", c(expression (italic ("F. occidentalis")*" observed"),
expression (italic ("M. pygmaeus")*" observed"),
expression (italic ("F. occidentalis")*" simulated"),
expression (italic ("M. pygmaeus")*" simulated")),
lty = c(1, 1, 1, 2),
col = c(1, 2, 1, 2),
lwd = c(2.5, 2.5, 1, 1),
box.lwd = 0, bty = "n")
# Plot C to F = same as A
par(opar)
My output doesn't give an error. I have used the exact same code before without any trouble, thus I restarted R, removed all objects, cleared all plots and restarted both RStudio and my computer.
Try to add xpd=TRUE in your legend statement. I.e.
legend("center", c(expression (italic ("F. occidentalis")*" observed"),
expression (italic ("M. pygmaeus")*" observed"),
expression (italic ("F. occidentalis")*" simulated"),
expression (italic ("M. pygmaeus")*" simulated")),
lty = c(1, 1, 1, 2),
col = c(1, 2, 1, 2),
lwd = c(2.5, 2.5, 1, 1),
box.lwd = 0, bty = "n", xpd=TRUE)
By default, the legend is cut off by the plotting region. This xpd parameter enables plotting outside the plot region. See e.g. ?par for more on xpd.
This is due to how the plot canvas is set up and how rescaling that device works. The way you do it, you add the legend in the plotting region of the top right plot. The plotting region is however not the complete device, but only the part inside the space formed by the axes. If you rescale, that plotting region will be rescaled as well. The margins around the plotting region don't change size though, so zooming in makes your plotting region so small that it doesn't fit the legend any longer. It is hidden by the margins around the plotting region.
For that reason AEBilgrau is very right you need to add xpd = TRUE. This allows the legend to extend outside of the plotting region, so it doesn't disappear behind the margins when resizing the plotting device.
I have a function that depends on distance and behaves different according to the direction (east or west) to where you evaluate it. Now I have two plots side by side, but I need to have them as one, where the labels of the axis are shared and the x axis label is centered. Here is an example of how the code looks right now:
x = (0:300)
par(mfrow=c(2,2))
Idriss70 = function(x){
exp(5.6315-0.4104*7-(2.9832-0.2339*7)*log(x+10)+0.00047*x+0.12)
}
plot(Idriss70(x), log = "x", type="l",xlim = c(300,1), xlab="Distancia [km]",ylab="PGA [g]", main="Aroma y Humayani extendida, Mw 7,0", col="green", panel.first = grid(equilogs = TRUE))
Idriss70 = function(x){
ifelse (x >= 0 & x<=3, exp(5.6315-0.4104*7-(2.9832-0.2339*7)*log(0+10)+0.00047*0+0.12),
exp(5.6315-0.4104*7-(2.9832-0.2339*7)*log(x+10)+0.00047*x+0.12))
}
plot(Idriss70(x), log = "x", type="l", xlab="Distancia [km]",ylab="PGA [g]", main="Aroma y Humayani extendida, Mw 7,0", col="green", panel.first = grid(equilogs = TRUE))
As you can see, the log scale of the plots don't allow "negative" values to be evaluated so I haven't been able to use only one plot.
How can I get this plot as one without using Illustrator or another graphics software, as I have to create lots of this ones for differente areas?
I haven't used ggplot in the past but I am willing to learn if necessary.
You can basically make one plot and mess around with fig so that you restrict the first plot to the left half of the device and the second to the right half
x <- 0:300
Idriss70 = function(x){
exp(5.6315-0.4104*7-(2.9832-0.2339*7)*log(x+10)+0.00047*x+0.12)
}
Idriss71 = function(x){
ifelse(x >= 0 & x<=3,
exp(5.6315-0.4104*7-(2.9832-0.2339*7)*log(0+10)+0.00047*0+0.12),
exp(5.6315-0.4104*7-(2.9832-0.2339*7)*log(x+10)+0.00047*x+0.12))
}
par(fig = c(0, .5, 0, 1), mar = c(5, 4, 4, 0), xaxs = 'i', ann = FALSE)
plot(Idriss70(x), log = "x", type="l", xlim = c(300,1),
col="green", axes = FALSE, panel.first = grid(equilogs = TRUE))
xx <- axis(1)
axis(2)
par(fig = c(.5, 1, 0, 1), new = TRUE, mar = c(5, 0, 4, 2))
plot(Idriss71(x), log = "x", type="l", col="green",
panel.first = grid(equilogs = TRUE), axes = FALSE)
axis(1, at = xx, labels = c('', xx[-1]))
title(xlab = "Distancia [km]", main = 'Aroma y Humayani extendida, Mw 7,0',
ylab = 'PGA [g]', outer = TRUE, line = -1.5)
good luck with ggplot. you'd probably have to summon #baptiste
well you could still use mfrow I suppose
graphics.off()
par(mfrow = c(1, 2), mar = c(5, 4, 4, 0), xaxs = 'i', ann = FALSE)
plot(Idriss70(x), log = "x", type="l", xlim = c(300,1),
col="green", axes = FALSE, panel.first = grid(equilogs = TRUE))
xx <- axis(1)
axis(2)
par(mar = c(5, 0, 4, 2))
plot(Idriss71(x), log = "x", type="l", col="green",
panel.first = grid(equilogs = TRUE), axes = FALSE)
axis(1, at = xx, labels = c('', xx[-1]))
title(xlab = "Distancia [km]", main = 'Aroma y Humayani extendida, Mw 7,0',
ylab = 'PGA [g]', outer = TRUE, line = -1.5)
I don't know how to change the code so that the y-axis in the barPlot shows completely? I expect it to show up to 10 as I have a 9.2 in my data points but it shows only up to 8. Any idea what's the hack to this?
Here's the code:
And here's what it shows:
just set the ylim = c(0, 10) like the way you changed the xlim
Whatever the axis that the groups go on isn't drawn by default, so a vertical bar plot won't have x-axis; horizontal won't have y-axis. You can add that of course. Use the return value of barplot:
par(mfrow = c(2, 1))
bp <- barplot(c(8, 5), width = .5, main = 'Feature Exploration', xlim = c(0,4), ylim = c(0, 10),
ylab = 'Errors (%)', xlab = 'ML Models', col = c('gray27','orangered4'))
## this will draw the x-axis but at points 1, 2, 3, ... which is not
## where the centers of your bars are plotted; you get that info in bp
axis(1)
bp <- barplot(c(8, 5), width = .5, main = 'Feature Exploration', xlim = c(0,4), ylim = c(0, 10),
ylab = 'Errors (%)', xlab = 'ML Models', col = c('gray27','orangered4'))
## so try again with a fancy axis, bp is a matrix containing the centers
## of the plotted bars
axis(1, at = bp, labels = c('Model1','Model2'), lwd = 0, lwd.ticks = 1, tcl = -.5)