Is there a way to draw the lines in such a way that they would start on the side of the points, or allow the symbols to be in foreground?
My solution was to make the symbols bigger and more visible.
Edit 1: it's for plot {graphics} of the R program.
Edit 2: the code per popular request.
legend(2,.4,bty='n', c('sugar','citrus','none'), pch=c('s','c','u'), pt.bg='white',lty= c(1,2,3), lwd=1.5, title="Condition",pt.cex=c(1.5),cex=1.5)
Edit 3: This is solved for plot(type='b') but somehow not for legend.
Thanks for reading!
The only thing I can come up with is to manually finagle the dash lengths until they end up looking the way you want them. For instance, this:
> plot(1,1)
> legend(c("A", "B"), col = 1:2, x = 1, y = .8, lty="99", pch=1:2)
produces the image below.
The lty parameter allows you to specify the lengths of lines and dashes as hex characters. In this case, it's saying to create a line of length 9 then create a space of length 9 then repeat. It looks like 9 is about the best fit to space around a normal pch symbol.
Note that you'd probably need to adjust this depending on the size of the image, symbol, etc. My advice ultimately would be to export the image from R and touch up the image to meet your needs in graphic editing software.
Going with the suggestion by #JeffAllen, here is a way to get what I think you might want. It requires modifying the legend() function to return the position of the points (these are given by x1 and y1 in body(legend)[[46]]).
legend2 <- legend
body(legend2)[[49]] <- quote(
invisible(list(rect = list(w = w, h = h, left = left, top = top),
text = list(x = xt, y = yt), points = list(x = x1, y = y1)))
)
Make a plot:
plot(-100:100, -100:100, type = "b")
While drawing the legend, draw white circles (pch = 21 with pt.bg = 'white') over the lines, and assign the values invisibly returned by legend2() to an object. Note also the changes to pt.lwd and pt.cex.
myLegend <- legend2(1, .8, bty = 'n', c('sugar','citrus','none'), pch = 21,
pt.bg = 'white', pt.lwd = 0, lty = c(1, 2, 3), lwd = 1.5, title = "Condition",
pt.cex = c(1.8), cex = 1.5)
Finally, draw the characters you'd like to use in the legend using points(), supplying the x and y values from the object myLegend.
points(myLegend$points$x, myLegend$points$y, pch = c('s','c','u'), cex = 1.5)
And this should get you something like:
You could also use the filled points offered by R (pch=21:25) and specify the fill color using pc.bg which gets passed to the points call when creating a legend.
plot(1,1)
legend(c("A", "B"), col = 1:2, x = 1, y = .8, lty=1, pt.bg=1:2, pch=21:22)
generates the following:
Related
I use the following script to generate a legend in R. But the legend box is too small... how do I increase the box width?
legend("topleft", lty = 1, legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),col = c("black","red","blue"))
You are probably resizing your graph after you plot it and the legend. If that is the case, and you want to keep the box, one option would be to plot the graph, resize it, and then generate the legend. Perhaps a better option would be to size the window to the desired width to start with:
# on Windows, you can use the `windows` function. elsewhere, try quartz or X11
windows(height = 7, width = 3.5)
plot(hp ~ mpg, data = mtcars)
leg <- legend("topleft", lty = 1,
legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),
col = c("black","red","blue"),
#plot = FALSE,
#bty = "n")
)
You can also define exactly where you want the box to fall by providing a pair of x and y coordinates to the legend function. Those values would represent the upper left and bottom right corners of the box. The legend function will actually generate the coordinates for the upper-left hand corner of the box along with the width and height. By default it returns them invisibly, but you can assign them to an object, and If you use the plot = FALSE, option to legend you can capture those coordinates and modify them as you wish without actually plotting the legend.
windows(height = 7, width = 3.5)
plot(hp ~ mpg, data = mtcars)
legend(x = c(9.46, 31), y = c(346.32, 298),
legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),
col = c("black","red","blue"),
lty = 1)
The legend function will actually generate the coordinates for the upper-left hand corner of the box (that's where I got 9.46 and 346.62) along with the width and height of the box. By default it returns them invisibly, but you can assign them to an object, and if you use the plot = FALSE, option to legend you can capture those coordinates and modify them as you wish without actually plotting the legend.
plot(hp ~ mpg, data = mtcars)
leg <- legend("topleft", lty = 1,
legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),
col = c("black","red","blue"),
plot = FALSE)
# adjust as desired
leftx <- leg$rect$left
rightx <- (leg$rect$left + leg$rect$w) * 1.2
topy <- leg$rect$top
bottomy <- (leg$rect$top - leg$rect$h) * 1
# use the new coordinates to define custom
legend(x = c(leftx, rightx), y = c(topy, bottomy), lty = 1,
legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),
col = c("black","red","blue"))
Part of the legend width is determined by the longest width of the labels you use, which is calculated via strwidth. Below an easy example how to halve or double the size by using legend(..., text.width = ...).
plot(1)
text = c("Sub_metering_1","Sub_metering_2","Sub_metering_3")
legend("topleft"
,lty = 1
,legend = text
,col = c("black","red","blue")
)
strwidth(text)
# [1] 0.1734099 0.1734099 0.1734099
# half the length
legend("bottomleft"
,lty = 1
,legend = text
,text.width = strwidth(text)[1]/2
,col = c("black","red","blue")
)
# double the length
legend("center"
,lty = 1
,legend = text
,text.width = strwidth(text)[1]*2
,col = c("black","red","blue")
)
Using this example:
x<-mtcars;
barplot(x$mpg);
you get a graph that is a lot of barplots from (0 - 30).
My question is how can you adjust it so that the y axis is (10-30) with a split at the bottom indicating that there was data below the cut off?
Specifically, I want to do this in base R program using only the barplot function and not functions from plotrix (unlike the suggests already provided). Is this possible?
This is not recommended. It is generally considered bad practice to chop off the bottoms of bars. However, if you look at ?barplot, it has a ylim argument which can be combined with xpd = FALSE (which turns on "clipping") to chop off the bottom of the bars.
barplot(mtcars$mpg, ylim = c(10, 30), xpd = FALSE)
Also note that you should be careful here. I followed your question and used 0 and 30 as the y-bounds, but the maximum mpg is 33.9, so I also clipped the top of the 4 bars that have values > 30.
The only way I know of to make a "split" in an axis is using plotrix. So, based on
Specifically, I want to do this in base R program using only the barplot function and not functions from plotrix (unlike the suggests already provided). Is this possible?
the answer is "no, this is not possible" in the sense that I think you mean. plotrix certainly does it, and it uses base R functions, so you could do it however they do it, but then you might as well use plotrix.
You can plot on top of your barplot, perhaps a horizontal dashed line (like below) could help indicate that you're breaking the commonly accepted rules of what barplots should be:
abline(h = 10.2, col = "white", lwd = 2, lty = 2)
The resulting image is below:
Edit: You could use segments to spoof an axis break, something like this:
barplot(mtcars$mpg, ylim = c(10, 30), xpd = FALSE)
xbase = -1.5
xoff = 0.5
ybase = c(10.3, 10.7)
yoff = 0
segments(x0 = xbase - xoff, x1 = xbase + xoff,
y0 = ybase-yoff, y1 = ybase + yoff, xpd = T, lwd = 2)
abline(h = mean(ybase), lwd = 2, lty = 2, col = "white")
As-is, this is pretty fragile, the xbase was adjusted by hand as it will depend on the range of your data. You could switch the barplot to xaxs = "i" and set xbase = 0 for more predictability, but why not just use plotrix which has already done all this work for you?!
ggplot In comments you said you don't like the look of ggplot. This is easily customized, e.g.:
library(ggplot2)
ggplot(x, aes(y = mpg, x = id)) +
geom_bar(stat = "identity", color = "black", fill = "gray80", width = 0.8) +
theme_classic()
At first I thought this would be trivial, but I could not figure out how to combine rectangles with lines in the legend of a lattice plot. Consider the following example:
library(latticeExtra)
xyplot(rnorm(10) ~ 1:10,
key=list(rectangles=list(size=2, border=F),
text=list(c("Zero", "One", "Two"), col="black"),
col=c("black", "lightgrey", "darkgrey"), divide=1, columns=1,
x=0.01, y=0.95, corner=c(0,1) ),
panel=function(x,...){
panel.abline(v=3, lty="dashed")
panel.xblocks(x,x>5, col="lightgrey")
panel.xblocks(x,x>7, col="darkgrey")
panel.xyplot(x, ...) } )
Instead of 3 rectangles, I would like to have 2 rectangles filled with the appropriate colours, and one dashed line above or below these two rectangles. If I provide a lines argument, then both lines and rectangles will be drawn for all elements (i.e. there will be 2 rectangles and 2 lines simultaneously next to each other).
How can I set up the legend key so that I get this mix of "symbols"? That is, how can I get one dashed line and two rectangles with the appropriate text and colours?
Any help is greatly appreciated! My apologies if this is trival. Please help me see the obvious! :)
This is a rather late answer but it is something I still do. One approach is to use auto.key in the function and then modify the lattice object with update(obj, key = newKey). A more general approach, as suggested by #josh-obrien, is to use the grid functions that under lattice. However, this typically requires empirical tweaking of the coordinates as can be seen in the need to use 3 decimal places of precision to place the dashed lines.
# relative position may be sensitive to absolute sizes
library(latticeExtra)
dev.new(width = 5, height = 5)
set.seed(1234)
# same code as in question, re-written a little bit
# using "transparent" for the 1st of the three rectangles
# using a grid call in the panel function to place the dashed line
xyplot(rnorm(10) ~ 1:10,
key = list(rectangles = list(size = 2, border = FALSE,
col = c("transparent", "lightgrey", "darkgrey")),
text = list(c("Zero", "One", "Two"), col = "black"),
columns = 1, corner = c(0.01, 0.95)),
panel = function(x,...) {
panel.abline(v = 3, lty = "dashed")
panel.xblocks(x, x > 5, col = "lightgrey")
panel.xblocks(x, x > 7, col = "darkgrey")
panel.xyplot(x, ...)
grid::grid.lines(c(0.04, 0.07), c(0.935, 0.935),
gp = gpar(lty = "dashed", col = "black"))
}
)
[![plot with combined elements in legend][1]][1]
[1]: https://i.stack.imgur.com/K7AJN.png
Consider the following plot:
par(xaxs='i',yaxs='i')
q1 <- c(1000000.0, 908364.8, 876009.1, 847892.8, 824808.3, 805416.2, 785266.2, 770997.1, 753908.6, 744599.9, 706777.6, 674659.9, 634654.4, 601440.4, 568259.7, 535361.3, 493679.9, 465526.5, 429766.6, 395244.7, 361483.2, 332136.6, 308574.5, 285500.6, 262166.2 ,237989.0 , 210766.1, 188578.1, 166762.3 , 140399.8 ,114865.5)
plot(q1, type = "l", lty = 1, lwd = 2, col = "darkolivegreen3", ylim = c(0,4*10^6), xlim = c(1,30), bty = "l")
text(30, q1[30], labels = "text", col = "gray36", cex = 0.8, pos = 4)
I would like to add the label "text" at the right of the last point of the green line (i.e. the point on the line with x = 30).
I tried the code above but the text doesn't show up! Any ideas how to solve that?
Thanks!
By default things in a plot are clipped to the plot region, you are not seeing the text because it has been clipped. You can either use the mtext function to explicitly place the text into the margin. Or if you specify par(xpd=NA) then the clipping will be turned off (well it will still clip to the device region) and the text plotted using the text function will now be plotted extending into the margin. Either way you will probably want to specify some space in the appropriate margin so there is room for the text to be and look nice. See ?par for how to specify the margin and more detail on clipping.
I just realized that this could be done using mtext:
mtext("text", side = 4, at = q1[30], las = 1)
I have been working on Venn Diagrams in GNU R. I have tried using the packages venneuler and VennDiagram. I find that VennDiagram has a lot more granular control, but it seems to lack the documentation to fill in all the details. The closest I can find is this PPT file.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041657/bin/1471-2105-12-35-S4.PPT which I found from the URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041657/
Here are my issues with using VennDiagram.
For the code
require(VennDiagram)
venn.diagram(list(B = 1:2000, A = 200:400),fill = c("yellow", "blue"),
alpha = c(0.8, 0.8), cex =1.5, cat.pos=0, cat.fontface = 4,
lty = 1, fontfamily =3, filename = "test001.jpeg");
(I had an image here, but since I am new I do not have rights to post the image. Please generate the image from the code above.)
I can make a subset (hence a circle within a circle). But I am not finding a way to do the following:
Make BC to show as the equal of B^C. No, a literal "B^C" does not work. I would think there is a way to relabel the sets in a different property, but I have not seen a way to do it.
To position the labels of B^C and A^C within the sets and not on the outside as currently shown. I tried cat.pos="inner" but that way not a valid property. I also tried cat.pos=c(0,0) in the hope that I could feed it as an X,Y where X & Y are from the center of the circle, but it did not produce any different results.
Thanks to DWin, here is the code to complete my diagram to the exercise.
Suppose that A ⊂ B. Show that Bc ⊂ Ac.
require(VennDiagram)
plot.new()
venn.plot <- venn.diagram(
x = list(B = 1:200, A = 20:40), category.names= expression(B, A),
fill = c("yellow", "blue"), alpha = c(0.8, 0.8), cex =1.5,
cat.pos=0, cat.dist=c(-.1, -.1), filename = NULL) ;
grid.draw(venn.plot); # grid graphic requires explicit print or draw operation
grid.text(expression(B^c),x=0.2,y=0.95)
grid.text(expression(A^c),x=0.16,y=0.95)
grid.text(expression(A^c),x=0.16,y=0.75)
Perhaps something like this:
venn.diagram(list(B = 1:200, A = 20:40), category.names= expression(B^c, A),
fill = c("yellow", "blue"), alpha = c(0.8, 0.8), cex =1.5, cat.pos=0,
cat.dist=c(.1, -.1), cat.fontface = 4,lty = 1, fontfamily =3,
filename = "test001.jpeg")
To get the labels inside the circles, supply 'cat.dist' with negative values. The trick is that the reference point is radial distance from the boundary at 12 o'clock rather than from the center. The documentation says that the category.names argument is interpreted with plotmath syntax. The superscript operation in plotmath is done with the "^" operator. I have here moved the A" inside while leaving the B^c outside to suggest that it is the area outside the B circle that is being labeled. (I also improved the plotting time by making the example smaller.) I tried drawing three labels but that does not seem to "part of the package".
Here's a way you can annotate with grid.text() on the screen device:
plot.new()
venn.plot <- venn.diagram(
x = list(B = 1:200, A = 20:40), category.names= expression(B^c, A),
fill = c("yellow", "blue"), alpha = c(0.8, 0.8), cex =1.5,
cat.pos=0, cat.dist=c(.05, -.1), filename = NULL) ;
grid.draw(venn.plot); # grid graphic requires explicit print or draw operation
grid.text("B",x=0.8)
# then you can save to file