I regularly do all kinds of scatter plots in R using the plot command.
Sometimes both, sometimes only one of the plot axes is labelled in scientific notation. I do not understand when R makes the decision to switch to scientific notation. Surprisingly, it often prints numbers which no sane human would write in scientific notation when labelling a plot, for example it labels 5 as 5e+00. Let's say you have a log-axis going up to 1000, scientific notation is unjustified with such "small" numbers.
I would like to suppress that behaviour, I always want R to display integer values. Is this possible?
I tried options(scipen=10) but then it starts writing 5.0 instead of 5, while on the other axis 5 is still 5 etc. How can I have pure integer values in my R plots?
I am using R 2.12.1 on Windows 7.
Use options(scipen=5) or some other high enough number. The scipen option determines how likely R is to switch to scientific notation, the higher the value the less likely it is to switch. Set the option before making your plot, if it still has scientific notation, set it to a higher number.
You can use format or formatC to, ahem, format your axis labels.
For whole numbers, try
x <- 10 ^ (1:10)
format(x, scientific = FALSE)
formatC(x, digits = 0, format = "f")
If the numbers are convertable to actual integers (i.e., not too big), you can also use
formatC(x, format = "d")
How you get the labels onto your axis depends upon the plotting system that you are using.
Try this. I purposely broke out various parts so you can move things around.
library(sfsmisc)
#Generate the data
x <- 1:100000
y <- 1:100000
#Setup the plot area
par(pty="m", plt=c(0.1, 1, 0.1, 1), omd=c(0.1,0.9,0.1,0.9))
#Plot a blank graph without completing the x or y axis
plot(x, y, type = "n", xaxt = "n", yaxt="n", xlab="", ylab="", log = "x", col="blue")
mtext(side=3, text="Test Plot", line=1.2, cex=1.5)
#Complete the x axis
eaxis(1, padj=-0.5, cex.axis=0.8)
mtext(side=1, text="x", line=2.5)
#Complete the y axis and add the grid
aty <- seq(par("yaxp")[1], par("yaxp")[2], (par("yaxp")[2] - par("yaxp")[1])/par("yaxp")[3])
axis(2, at=aty, labels=format(aty, scientific=FALSE), hadj=0.9, cex.axis=0.8, las=2)
mtext(side=2, text="y", line=4.5)
grid()
#Add the line last so it will be on top of the grid
lines(x, y, col="blue")
You can use the axis() command for that, eg :
x <- 1:100000
y <- 1:100000
marks <- c(0,20000,40000,60000,80000,100000)
plot(x,y,log="x",yaxt="n",type="l")
axis(2,at=marks,labels=marks)
gives :
EDIT : if you want to have all of them in the same format, you can use the solution of #Richie to get them :
x <- 1:100000
y <- 1:100000
format(y,scientific=FALSE)
plot(x,y,log="x",yaxt="n",type="l")
axis(2,at=marks,labels=format(marks,scientific=FALSE))
You could try lattice:
require(lattice)
x <- 1:100000
y <- 1:100000
xyplot(y~x, scales=list(x = list(log = 10)), type="l")
The R graphics package has the function axTicks that returns the tick locations of the ticks that the axis and plot functions would set automatically. The other answers given to this question define the tick locations manually which might not be convenient in some situations.
myTicks = axTicks(1)
axis(1, at = myTicks, labels = formatC(myTicks, format = 'd'))
A minimal example would be
plot(10^(0:10), 0:10, log = 'x', xaxt = 'n')
myTicks = axTicks(1)
axis(1, at = myTicks, labels = formatC(myTicks, format = 'd'))
There is also an log parameter in the axTicks function but in this situation it does not need to be set to get the proper logarithmic axis tick location.
Normally setting axis limit # max of your variable is enough
a <- c(0:1000000)
b <- c(0:1000000)
plot(a, b, ylim = c(0, max(b)))
Related
Let's consider a vector and plot it.
s1 <- sample(100:1000,32,replace = T)
plot(s1)
The plot I get has a Y-Axis that ranges from 0-1000 with points in the intervals of 200 (0,200,400,600,800,1000) and this is happening implicitly.
If I use ylim argument, apparently or to be honest, evidently, I can now have a custom range,
plot(s1,ylim = c(0,1500))
The points on Y Axis now are 0-1500 as indicated but with the points in the intervals of 500 (0,500,1000,1500), this is happening without my control.
My question, how can I have custom points with custom intervals on the X or Y axis?
use axis() to set your limits : on either x, y, or both
s1 <- sample(100:1000,32,replace = T)
plot(s1, yaxt = "n") # `yaxt` prevents y-axis labels to be printed
axis(2, yaxp=c(10, 1000, 10), las=2) # 'las' helps to align the tick mark labels along the axis or perpendicular
# 'yaxp' helps to set the break points you desire. Learn more from ?par
How can I change the spacing of tick marks on the axis of a plot?
What parameters should I use with base plot or with rgl?
There are at least two ways for achieving this in base graph (my examples are for the x-axis, but work the same for the y-axis):
Use par(xaxp = c(x1, x2, n)) or plot(..., xaxp = c(x1, x2, n)) to define the position (x1 & x2) of the extreme tick marks and the number of intervals between the tick marks (n). Accordingly, n+1 is the number of tick marks drawn. (This works only if you use no logarithmic scale, for the behavior with logarithmic scales see ?par.)
You can suppress the drawing of the axis altogether and add the tick marks later with axis().
To suppress the drawing of the axis use plot(... , xaxt = "n").
Then call axis() with side, at, and labels: axis(side = 1, at = v1, labels = v2). With side referring to the side of the axis (1 = x-axis, 2 = y-axis), v1 being a vector containing the position of the ticks (e.g., c(1, 3, 5) if your axis ranges from 0 to 6 and you want three marks), and v2 a vector containing the labels for the specified tick marks (must be of same length as v1, e.g., c("group a", "group b", "group c")). See ?axis and my updated answer to a post on stats.stackexchange for an example of this method.
With base graphics, the easiest way is to stop the plotting functions from drawing axes and then draw them yourself.
plot(1:10, 1:10, axes = FALSE)
axis(side = 1, at = c(1,5,10))
axis(side = 2, at = c(1,3,7,10))
box()
I have a data set with Time as the x-axis, and Intensity as y-axis. I'd need to first delete all the default axes except the axes' labels with:
plot(Time,Intensity,axes=F)
Then I rebuild the plot's elements with:
box() # create a wrap around the points plotted
axis(labels=NA,side=1,tck=-0.015,at=c(seq(from=0,to=1000,by=100))) # labels = NA prevents the creation of the numbers and tick marks, tck is how long the tick mark is.
axis(labels=NA,side=2,tck=-0.015)
axis(lwd=0,side=1,line=-0.4,at=c(seq(from=0,to=1000,by=100))) # lwd option sets the tick mark to 0 length because tck already takes care of the mark
axis(lwd=0,line=-0.4,side=2,las=1) # las changes the direction of the number labels to horizontal instead of vertical.
So, at = c(...) specifies the collection of positions to put the tick marks. Here I'd like to put the marks at 0, 100, 200,..., 1000. seq(from =...,to =...,by =...) gives me the choice of limits and the increments.
And if you don't want R to add decimals or zeros, you can stop it from drawing the x axis or the y axis or both using ...axt. Then, you can add your own ticks and labels:
plot(x, y, xaxt="n")
plot(x, y, yaxt="n")
axis(1 or 2, at=c(1, 5, 10), labels=c("First", "Second", "Third"))
I just discovered the Hmisc package:
Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.
library(Hmisc)
plot(...)
minor.tick(nx=10, ny=10) # make minor tick marks (without labels) every 10th
I am trying to get only power 10 scale on the y axis, and I have tried many approaches offered on StackOverflow but none produce what I want.
I want to define the scale of y-axis to start from 10^2 and then next tick be at 10^4 and then on 10^6.
I have tried xaxt and at and axis and everything mentioned here, but none work for 10^x..
The plot.default() function provides a log argument which can be used to easily get a logarithmic scale of the x-axis, y-axis, or both. For example:
x <- 2:6;
y <- 10^x;
plot(x,y,log='y');
If you want to control the y-axis ticks, you can override the default axis and draw your own in the normal way:
## generate data
x <- 2:6;
y <- 10^x;
## precompute plot parameters
xlim <- c(2,6);
ylim <- c(10^2,10^6);
xticks <- 2:6;
yticks <- 10^seq(2L,6L,2L);
## draw plot
plot(NA,xlim=xlim,ylim=ylim,log='y',axes=F,xaxs='i',yaxs='i',xlab='x',ylab='y');
abline(v=xticks,col='lightgrey');
abline(h=yticks,col='lightgrey');
axis(1L,xticks,cex.axis=0.7);
axis(2L,yticks,sprintf('10^%d',as.integer(log10(yticks))),las=2L,cex.axis=0.7);
##axis(2L,yticks,sprintf('%.0e',yticks),las=2L,cex.axis=0.7); ## alternative
points(x,y,pch=19L,col='red',xpd=NA);
axis() works:
x <- 2:6
y <- 10 ^ x
plot(x, y, yaxt = "n")
axis(2, at = 10^(c(2, 4, 6)))
The only problem is that, this is certainly not a good way for presentation. Do you know how fast 1e+n grows?? As you have already seen in the plot, the ticks for 1e+2 and 1e+4 almost coincide, because 1e+6 is so big. If your data range from 1 ~ 1e+8 or even greater, then you'd better plot them on log scale.
plot(x, log10(y), yaxt = "n")
axis(2, at = c(2,4,6))
I regularly do all kinds of scatter plots in R using the plot command.
Sometimes both, sometimes only one of the plot axes is labelled in scientific notation. I do not understand when R makes the decision to switch to scientific notation. Surprisingly, it often prints numbers which no sane human would write in scientific notation when labelling a plot, for example it labels 5 as 5e+00. Let's say you have a log-axis going up to 1000, scientific notation is unjustified with such "small" numbers.
I would like to suppress that behaviour, I always want R to display integer values. Is this possible?
I tried options(scipen=10) but then it starts writing 5.0 instead of 5, while on the other axis 5 is still 5 etc. How can I have pure integer values in my R plots?
I am using R 2.12.1 on Windows 7.
Use options(scipen=5) or some other high enough number. The scipen option determines how likely R is to switch to scientific notation, the higher the value the less likely it is to switch. Set the option before making your plot, if it still has scientific notation, set it to a higher number.
You can use format or formatC to, ahem, format your axis labels.
For whole numbers, try
x <- 10 ^ (1:10)
format(x, scientific = FALSE)
formatC(x, digits = 0, format = "f")
If the numbers are convertable to actual integers (i.e., not too big), you can also use
formatC(x, format = "d")
How you get the labels onto your axis depends upon the plotting system that you are using.
Try this. I purposely broke out various parts so you can move things around.
library(sfsmisc)
#Generate the data
x <- 1:100000
y <- 1:100000
#Setup the plot area
par(pty="m", plt=c(0.1, 1, 0.1, 1), omd=c(0.1,0.9,0.1,0.9))
#Plot a blank graph without completing the x or y axis
plot(x, y, type = "n", xaxt = "n", yaxt="n", xlab="", ylab="", log = "x", col="blue")
mtext(side=3, text="Test Plot", line=1.2, cex=1.5)
#Complete the x axis
eaxis(1, padj=-0.5, cex.axis=0.8)
mtext(side=1, text="x", line=2.5)
#Complete the y axis and add the grid
aty <- seq(par("yaxp")[1], par("yaxp")[2], (par("yaxp")[2] - par("yaxp")[1])/par("yaxp")[3])
axis(2, at=aty, labels=format(aty, scientific=FALSE), hadj=0.9, cex.axis=0.8, las=2)
mtext(side=2, text="y", line=4.5)
grid()
#Add the line last so it will be on top of the grid
lines(x, y, col="blue")
You can use the axis() command for that, eg :
x <- 1:100000
y <- 1:100000
marks <- c(0,20000,40000,60000,80000,100000)
plot(x,y,log="x",yaxt="n",type="l")
axis(2,at=marks,labels=marks)
gives :
EDIT : if you want to have all of them in the same format, you can use the solution of #Richie to get them :
x <- 1:100000
y <- 1:100000
format(y,scientific=FALSE)
plot(x,y,log="x",yaxt="n",type="l")
axis(2,at=marks,labels=format(marks,scientific=FALSE))
You could try lattice:
require(lattice)
x <- 1:100000
y <- 1:100000
xyplot(y~x, scales=list(x = list(log = 10)), type="l")
The R graphics package has the function axTicks that returns the tick locations of the ticks that the axis and plot functions would set automatically. The other answers given to this question define the tick locations manually which might not be convenient in some situations.
myTicks = axTicks(1)
axis(1, at = myTicks, labels = formatC(myTicks, format = 'd'))
A minimal example would be
plot(10^(0:10), 0:10, log = 'x', xaxt = 'n')
myTicks = axTicks(1)
axis(1, at = myTicks, labels = formatC(myTicks, format = 'd'))
There is also an log parameter in the axTicks function but in this situation it does not need to be set to get the proper logarithmic axis tick location.
Normally setting axis limit # max of your variable is enough
a <- c(0:1000000)
b <- c(0:1000000)
plot(a, b, ylim = c(0, max(b)))
While plotting histogarm, scatterplots and other plots with axes scaled to logarithmic scale in R, how is it possible to use labels such as 10^-1 10^0 10^1 10^2 10^3 and so on instead of the axes showing just -1, 0, 1, 2, 3 etc. What parameters should be added to the commands such as hist(), plot() etc?
Apart from the solution of ggplot2 (see gsk3's comment), I would like to add that this happens automatically in plot() as well when using the correct arguments, eg :
x <- 1:10
y <- exp(1:10)
plot(x,y,log="y")
You can use the parameter log="x" for the X axis, or log="xy" for both.
If you want to format the numbers, or you have the data in log format, you can do a workaround using axis(). Some interesting functions :
axTicks(x) gives you the location of the ticks on the X-axis (x=1) or Y-axis (x=2)
bquote() converts expressions to language, but can replace a variable with its value. More information on bquote() in the question Latex and variables in plot label in R? .
as.expression() makes the language object coming from bquote() an expression. This allows axis() to do the formatting as explained in ?plotmath. It can't do so with language objects.
An example for nice formatting :
x <- y <- 1:10
plot(x,y,yaxt="n")
aty <- axTicks(2)
labels <- sapply(aty,function(i)
as.expression(bquote(10^ .(i)))
)
axis(2,at=aty,labels=labels)
Which gives
Here is a different way to draw this type of axis:
plot(NA, xlim=c(0,10), ylim=c(1, 10^4), xlab="x", ylab="y", log="y", yaxt="n")
at.y <- outer(1:9, 10^(0:4))
lab.y <- ifelse(log10(at.y) %% 1 == 0, at.y, NA)
axis(2, at=at.y, labels=lab.y, las=1)
EDIT: This is also solved in latticeExtra with scale.components
In ggplot2 you just can add a
... +
scale_x_log10() +
scale_y_log10(limits = c(1e-4,1), breaks=c(1e-4,1e-3,1e-2,0.1,1)) + ...
to scale your axis, Label them and add custom breaks.