Earlier I asked about creating a gradient of n values in base graphics (LINK). Now I'd like to create a gradient legend that goes with it. My ideal would be something like ggplot2's gradient legends:
Here's some code similar to what I'm working with:
colfunc <- colorRampPalette(c("red", "blue"))
plot(1:20, 1:20, pch = 19, cex=2, col = colfunc(20))
Here is an example of how to build a legend from first principles using rasterImage from grDevices and layout to split the screen
layout(matrix(1:2,ncol=2), width = c(2,1),height = c(1,1))
plot(1:20, 1:20, pch = 19, cex=2, col = colfunc(20))
legend_image <- as.raster(matrix(colfunc(20), ncol=1))
plot(c(0,2),c(0,1),type = 'n', axes = F,xlab = '', ylab = '', main = 'legend title')
text(x=1.5, y = seq(0,1,l=5), labels = seq(0,1,l=5))
rasterImage(legend_image, 0, 0, 1,1)
Late to the party, but here is a base version presenting a legend using discrete cutoffs. Thought it might be useful for future searchers.
layout(matrix(1:2,nrow=1),widths=c(0.8,0.2))
colfunc <- colorRampPalette(c("white","black"))
par(mar=c(5.1,4.1,4.1,2.1))
plot(1:10,ann=FALSE,type="n")
grid()
points(1:10,col=colfunc(10),pch=19,cex=1.5)
xl <- 1
yb <- 1
xr <- 1.5
yt <- 2
par(mar=c(5.1,0.5,4.1,0.5))
plot(NA,type="n",ann=FALSE,xlim=c(1,2),ylim=c(1,2),xaxt="n",yaxt="n",bty="n")
rect(
xl,
head(seq(yb,yt,(yt-yb)/10),-1),
xr,
tail(seq(yb,yt,(yt-yb)/10),-1),
col=colfunc(10)
)
mtext(1:10,side=2,at=tail(seq(yb,yt,(yt-yb)/10),-1)-0.05,las=2,cex=0.7)
And an example image:
The following creates a gradient color bar with three pinpoints without any plot beforehand and no alien package is needed. Hope it is useful:
plot.new()
lgd_ = rep(NA, 11)
lgd_[c(1,6,11)] = c(1,6,11)
legend(x = 0.5, y = 0.5,
legend = lgd_,
fill = colorRampPalette(colors = c('black','red3','grey96'))(11),
border = NA,
y.intersp = 0.5,
cex = 2, text.font = 2)
As a refinement of #mnel's great answer, inspired from another great answer of #Josh O'Brien, here comes a way to display the gradient legend inside the plot.
colfunc <- colorRampPalette(c("red", "blue"))
legend_image <- as.raster(matrix(colfunc(20), ncol=1))
## layer 1, base plot
plot(1:20, 1:20, pch=19, cex=2, col=colfunc(20), main='
Awesome gradient legend inside')
## layer 2, legend inside
op <- par( ## set and store par
fig=c(grconvertX(c(0, 10), from="user", to="ndc"), ## set figure region
grconvertY(c(4, 20.5), from="user", to="ndc")),
mar=c(1, 1, 1, 9.5), ## set margins
new=TRUE) ## set new for overplot w/ next plot
plot(c(0, 2), c(0, 1), type='n', axes=F, xlab='', ylab='') ## ini plot2
rasterImage(legend_image, 0, 0, 1, 1) ## the gradient
lbsq <- seq.int(0, 1, l=5) ## seq. for labels
axis(4, at=lbsq, pos=1, labels=F, col=0, col.ticks=1, tck=-.1) ## axis ticks
mtext(sq, 4, -.5, at=lbsq, las=2, cex=.6) ## tick labels
mtext('diff', 3, -.125, cex=.6, adj=.1, font=2) ## title
par(op) ## reset par
Related
I am mapping using the "oce" package in R and want to add color to the ocean. I can manipulate the land color but not the ocean, and the mapping function omits "bg" to add background color. Here is my current code and parameters:
library(oce)
library(ocedata)
data("coastlineWorldFine")
par(mar=c(2, 2, 1, 1))
lonlim <- c(-79, -76)
latlim <- c(33, 35)
mapPlot(coastlineWorldFine,
projection="+proj=moll",
col = "lightgray",
longitudelim=lonlim,
latitudelim=latlim,
grid = FALSE,
bg = "lightblue")
Any suggestions on how to change the color of the ocean from white to a light blue?
Thanks!
Bit of a hack, but you can plot a rectangle the same size as the plotting area, then use par(new = TRUE) to plot mapPlot on top:
par(mar=c(2, 2, 1, 1))
plot(0, 0, type="n", ann=FALSE, axes=FALSE)
user <- par("usr")
rect(user[1], user[3], user[2], user[4],
col="lightblue", border=NA)
par(new = TRUE)
lonlim <- c(-79, -76)
latlim <- c(33, 35)
mapPlot(coastlineWorldFine,
projection="+proj=moll",
col = "lightgray",
longitudelim=lonlim,
latitudelim=latlim,
grid = FALSE)
I would like to use the function abline to plot several lines which should be made transparent but I am stuck.
Currently I have this code:
plot(x=NA, type="n", ylim=c(1, 9), xlim=c(1, 4), xlab="x-value",
ylab="y-value", cex.axis = 1, cex.lab = 1)
for (i in 1:nrow(one_hundred_regressions)) {abline(coef=one_hundred_regressions[i,],
col = "red")}
Use adjustcolor changing the alpha value to whatever degree of transparency you want:
plot(1:10)
abline(v = 1:10, col = adjustcolor("red", alpha = 0.3))
You may use RGB colors "#RRGGBBaa", where aa is the alpha value for transparency. Example:
plot(1:10, type="n")
Map(function(x, y, z) abline(coef=c(x, y), col=z, lwd=2), 2:4, 2/(2:4)^2,
c("#AA000066", "#00AA0066", "#0000AA66"))
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 would like to control the height of the colorbar to the extent of the plot window.
For example, if I use:
if (dev.cur() == 1) x11(width=10,height=9)
par(mfrow=c(2,1))
How can I increase the height of the colorbar to be same height as the plots window? e.g.
plot(r, legend.only=TRUE, legend.width=1.4, legend.shrink=1,
col=colorRampPalette(c("darkred", "red3", "orange2", "orange",
"yellow", "lightskyblue","steelblue3",
"royalblue3", "darkblue"))(12),
breaks=brks, axis.args=list(at=seq(80, 205, by=10),
labels=seq(80, 205, by=10), cex.axis=0.9),
legend.args=list(text='Precipitation (mm)', side=4, font=2,
line=2.3, cex=0.8))
Many thanks
AZ.
If I understand correctly, you want to plot a full-height legend beside two plots whose layout is defined by par(mfrow=c(2, 1).
One way to achieve this is to generate the two plots, then set par(new=FALSE) and plot the raster again with legend.only=TRUE.
library(raster)
r <- raster(matrix(runif(100), ncol=10))
# Set layout; ensure appropriate space at right for legend
par(mfrow=c(2, 1), mar=c(2, 3, 1, 3))
# Plot raster
plot(r, legend=FALSE, zlim=c(0, 1), las=1)
# Plot second object
plot(runif(10), runif(10), pch=21, cex=2, las=1,
bg=rev(terrain.colors(10)[sample(10, 10, replace=T)]))
# Revert to c(1, 1) layout and adjust legend margins
par(mfrow=c(1, 1), mar=c(2, 0, 1, 0), new=FALSE)
# Plot legend
plot(r, legend.only=TRUE, legend.shrink=1, legend.width=2, zlim=c(0, 1),
axis.args=list(at=pretty(0:1), labels=pretty(0:1)),
legend.args=list(text='Whatever', side=4, font=2, line=2.3))
If you are plotting multiple raster objects with matching extents and resolution, you might consider rasterVis::levelplot, which has a RasterStack method:
library(rasterVis)
s <- stack(replicate(2, raster(matrix(runif(100), nc=10))))
levelplot(s, layout=c(1, 2), names.attr=c('One', 'Two'),
at=seq(0, 1, length.out=100),
par.strip.text=list(font=2, cex=1.2))
# Plotting titles for vertical colorkeys is a little fiddly...
grid::grid.text('Precipitation (mm)', rot=90, y=unit(0.5, "npc"),
x=unit(0.95, "npc"))
You can suppress panel labels with par.strip.text=list(cex=0), and specify a colour ramp with col.regions:
levelplot(s, layout=c(1, 2),
col.regions=colorRampPalette(c('darkred', 'red3', 'orange2', 'orange',
'yellow', 'lightskyblue', 'steelblue3',
'royalblue3', 'darkblue')),
at=seq(0, 1, length.out=100), par.strip.text=list(cex=0),
scales=list(alternating=FALSE))
# Also demonstrating how to adjust fontface and size for legend title
grid::grid.text('Precipitation (mm)', y=unit(0.5, "npc"),
rot=90, x=unit(0.95, "npc"), gp=gpar(fontsize=14, font=2))
I am trying to remove all margins and the "figure region" of a plot in R, so that the plot region comprises the entire graphic device. I thought the code below would do it, but there is still a border around my plot (wider on left/bottom, thinner on top/right). Thanks
par(oma=c(0, 0, 0, 0))
par(mar=c(0, 0, 0, 0))
par(plt=c(0, 1, 0, 1))
Thought I would add a picture to show my progress. The xaxs and yaxs removed nearly all border from the top and right- there is still a border on the left and bottom.
The relevant portion of my script is below.
png("Test.png",
width = 256, height = 256,
units = "px", pointsize = 6.4,
bg = "black", res = NA)
par(mar=c(0, 0, 0, 0), xaxs='i', yaxs='i')
smoothScatter(lhb$px, lhb$pz, nrpoints=0, xlim=c(-3,3), ylim=c(0,5),
main="", xlab="", ylab="", axes=FALSE,
colramp=colorRampPalette(c("black", "#202020", "#736AFF", "cyan", "yellow", "#F87431", "#FF7F00", "red", "#7E2217"))
)
segments(.83, 1.597, .83, 3.436, col = par("fg"), lty = par("lty"), lwd = par("lwd"))
segments(-.83, 1.597, -.83, 3.436, col = par("fg"), lty = par("lty"), lwd = par("lwd"))
segments(-.83, 3.436, .83, 3.436, col = par("fg"), lty = par("lty"), lwd = par("lwd"))
segments(-.83, 1.597, .83, 1.597, col = par("fg"), lty = par("lty"), lwd = par("lwd"))
dev.off()
One issue is fundamentally not getting what plt does. From ?par we have:
‘plt’ A vector of the form ‘c(x1, x2, y1, y2)’ giving the
coordinates of the plot region as fractions of the current
figure region.
So your plot region is of zero size if you do par(plt=c(1, 1, 1, 1)), so that doesn't seem to be the way to go. This is because the figure region contains the plot region.
This plot seems to cover the entire region, without any margins:
op <- par(mar = rep(0, 4))
plot(1:10)
par(op)
it covers it so well you can't see the axes or the box:
This assumes the default for 0 outer margin (oma). Is this what you were looking for?
We can see that just adjusting the plot margins, as above, we also change the plt parameter as a side effect:
> par("plt")
[1] 0.1173174 0.9399106 0.1457273 0.8828467
> op <- par(mar = rep(0, 4))
> par("plt")
[1] 0 1 0 1
> par(op)
> par("plt")
[1] 0.1173174 0.9399106 0.1457273 0.8828467
indicating that simply setting the plot margins is sufficient to get a plot/figure region encompassing the entire device.
Of course, there is still a bit of internal padding that insures the ranges of the axes are slightly large than the range of the data in both the x and y coordinates. But you can control this with xaxs and yaxs --- see ?par
Update: As the OP has shown the sort of figure they are trying to produce without margins, I can provide a reproducible example:
set.seed(1)
dat <- matrix(rnorm(100*100), ncol = 100, nrow = 100)
layout(matrix(1:2, ncol = 2))
image(dat)
op <- par(mar = rep(0, 4))
image(dat)
par(op)
layout(1)
which gives for comparison:
and showing just the full plotting region:
Try setting the clip region parameter 'xpd' to NA ( clipped to device).
par(xpd = NA)