This has certainly been asked before, but I can't find a solution. I would like to plot some data with a perfect square as bounding box. With par(pty="s") this is easy, but once I save the plot as a pdf file, the square is lost. As I understand, this is because pdf() uses paper="special" as default and thus respects width and height (which does not give a perfect square since we have axis labels). But specifying other paper options did not help.
## the bounding rectangle in the following plot is a perfect square...
U <- matrix(runif(1000), ncol=2)
par(pty="s")
plot(U, type="p", xlab="U_1", ylab="U_2")
## ... however, not anymore if the plot is generated as a .pdf
pdf(file="U.pdf", width=6, height=6)
par(pty="s")
plot(U, type="p", xlab="U_1", ylab="U_2")
dev.off()
Related
In R, I have a raster object generated from a kernel density analysis using the ks package. I convert this into a raster object (from the raster package) and try to draw that raster object to a PNG using plot(). I want the png to have exactly one pixel for every pixel in the raster object. Simple enough, right? By default of course, I get all sorts of extraneous junk added to the plot. I can remove most of this using the various settings in plot() or par(), but no matter what I do, I don't seem able to get rid of the space formerly taken up by the legend on the right side of the plot.
library('ks')
library('raster')
# generate the data
set.seed(1)
x = matrix(rnorm(1000,1,0.5),500)
xpix = 100
ypix = 100
# calculate the density function
k = kde(
x,
H=matrix(c(0.1,0,0,0.1),2),
xmin=c(0,0),
xmax=c(1,1),
gridsize=c(xpix,ypix)
)
# convert to raster
r = raster(k)
# plot the image to PNG
png('file.png',width=xpix,height=ypix)
par(
mar=c(0,0,0,0),
bty='n',
bg='black',
plt=c(0,1,0,1)
)
plot(
r,
legend=FALSE,
axes=FALSE,
plt=c(0,1,0,1)
)
# see that 'plt' did not change
print(par())
dev.off()
If I check par before closing the device, I can see that the 'plt' value is not what I set it to; it shows the right margin, where the plotting area has been nudged over to make space for the non-legend. Sample code is above, and the image it generates is linked to here.
Incidentally, I was able to achieve the correct effect with the image() function instead of plot(), though that introduced it's own problems, namely that transparency no longer worked. Can I solve this with plot()? It's very frustrating that I'm so close but just can't seem to change the size of the plot area! I don't want to use another graphics package if there is any way to make the base function work.
I have tried to plot a series of points in R, and I use type="b" as a plot option. However, there is a lot of padding (white space) between the points and the lines between them, so much that the line disappears entirely between some points. Her is a picture of how it looks:
I have tried to make the points smaller with the cex plot option, but this does not help, as it only changes the size of the points and not where the lines between the points between these starts and ends. I do not know if this makes a difference, but the symbols I am using are pch=1.
I am interested in knowing if it is possible to reduce this padding, and how you do so. I am not interested in using type=o as a plot option instead.
Any particular reason why you don't want to use type="o"? It seems like the easiest way to get the effect you want:
# Fake data
set.seed(10)
dfs = data.frame(x=1:10, y=rnorm(10))
plot(y~x,data=dfs, type="o", pch=21, bg='white')
pch=21 is a circle marker like pch=1, but with both border and fill. We set the fill to white with bg="white" to "cover up" the lines that go through the point markers.
You can also use cex to change the marker size to avoid overlap and make the lines between nearby points visible:
set.seed(10)
dfs = data.frame(x=1:100, y=cumsum(rnorm(100)))
plot(y~x,data=dfs, type="o", pch=21, bg="white", cex=0.6)
Using a dataframe named dfs this seems to deliver a mechanism for adjusting the surrounding "white halo" to whatever size of point an halo you want by adjusting the 'cex' values of the white and black points :
plot(y~x,data=dfs, type="l")
with(dfs, points(x,y, pch=16,col="white",cex=1.4))
with(dfs, points(x,y,cex=1) )
I am trying to remove all grid lines outside the graph. I noticed that behavior in R is not deterministic, i.e., sometimes grid lines are inside the graph only (as I want), but sometimes it spans an entire figure (see sample). I'd like to always put grid lines inside.
I read grid manual, but could not find an option to do so. abline() also puts grid lines across an entire figure.
The code I am using is
plot(xrange, yrange, type="n", xlab="X", ylab="Y", xlim=c(200,1500), ylim=c(0,10000))
...
grid(lty=3, col="gray")
Any help is appreciated. Thanks,
Nodir
When I have had this problem it is because par(xpd=TRUE) is somewhere in the code. Try setting par(xpd=FALSE) before using grid() and then par(xpd=TRUE). The sample code was used to generate the same the two plots, one of which has the grid lines extending outside of the plot region.
set.seed(1)
x <- rnorm(100)
y <- rnorm(100)
# scatter plot with gridlines inside
par(xpd=FALSE) # do not plot outside the plot region
plot(x,y)
grid(lwd=2)
# scatterplot with gridlines outside the region
par(xpd=TRUE) # plot outside the plot region
plot(x,y)
grid(lwd=2)
I'm trying to create a scatter plot + linear regression line in R 3.0.3. I originally tried to create it with the following simple call to plot:
plot(hops$average.temperature, hops$percent.alpha.acids)
This created this first plot:
As you can see, the scales of the Y and X axes differ. I tried fixing this using the asp parameter, as follows:
plot(hops$average.temperature, hops$percent.alpha.acids, asp=1, xaxp=c(13,18,5))
This produced this second plot:
Unfortunately, setting asp to 1 appears to have compressed the X axis while using the same amount of space, leaving large areas of unused whitespace on either side of the data. I tried using xlim to constrain the size of the X-axis, but asp seemed to overrule it as it didn't have any effect on the plot.
plot(hops$average.temperature, hops$percent.alpha.acids, xlim=c(13,18), asp=1, xaxp=c(13,18,5))
Any suggestions as to how I could get the axes to be on the same scale without creating large amounts of whitespace?
Thanks!
One solution would be to use par parameter pty and set it to "s". See ?par:
pty
A character specifying the type of plot region to be used; "s"
generates a square plotting region and "m" generates the maximal
plotting region.
It forces the plot to be square (thus conteracting the side effect of asp).
hops <- data.frame(a=runif(100,13,18),b=runif(100,2,6))
par(pty="s")
plot(hops$a,hops$b,asp=1)
I agree with plannapus that the issue is with your plotting area. You can also fix this within the device size itself by ensuring that you plot to a square region. The example below opens a plotting device with square dimension; then the margins are also set to maintain these proportions:
Example:
n <- 20
x <- runif(n, 13, 18)
y <- runif(n, 2, 6)
png("plot.png", width=5, height=5, units="in", res=200)
par(mar=c(5,5,1,1))
plot(x, y, asp=1)
dev.off()
How can I use R to make axes always square in scatter plots? for example in:
> plot(iris)
or
> plot(iris$Petal.Width, iris$Petal.Length)
I'd like the axes to be square, i.e. the same length and tick labels for the x and y axes.
The current proposed answer does not work: the call,
plot(iris$Petal.Width, iris$Petal.Length, xlim=c(0,10), ylim=c(0,10), asp=1)
Generates:
which is not square, and does not have the same axis ticks and tick labels. The spaces between the x tick labels must be the same and the plot should be square, not rectangular.
You need to also set pty="s" in the graphics parameters to make the plot region square (independent of device size and limits):
par(pty="s")
plot(iris$Petal.Width, iris$Petal.Length, asp=1)
lines(2+c(0,1,1,0,0),3+c(0,0,1,1,0)) # confirm square visually
First of all, for me the plot already comes out square (big image). Clearly for you this is not the case, and you might need to make plots larger than the screen anyhow.
So, the size of the plot is controlled by the size of the output area, ie the plot window, the image file, or whatever else. Using Rstudio, you can use the built-in GUI the specify plot size. If you insist on using the base R console, you'll need to manually do the exporting. First open the file:
png("image.png", width=600, height=600)
This will open an image file in the working directory with equal proportions. Now plot:
x = iris$Petal.Width
y = iris$Petal.Length
all = c(x,y)
range = c(min(all), max(all))
plot(x, y, xlim=range, ylim=range)
And close the file:
dev.off()
The result: