I am using the following couple of lines to produce the below plot from rows of two 4X10 Matrix d1, and d2 in one graph:
plot(as.matrix(d1[2,]), as.matrix(d2[2,]), type="o", col="red",
ann=FALSE, pch=17, log = 'y',lty=4, axes=FALSE, las=2) +
lines(as.matrix(d1[1,]),as.matrix(d2[1,]), type="o", col="blue",
ann=FALSE, pch=15, lty=4)
x_axis_labels <- c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
axis(1,labels = x_axis_labels, at = x_axis_labels)
y_axis_labels <- c(3e+4, 6e+4,2e+5,3e+5, 6e+5, 2e+6,5e+6)
axis(2,labels = y_axis_labels, at = y_axis_labels, las=2)
grid()
Which produces the following:
But what I like to have is to have the grid to start from all the labels on each axis. At the moment it only starts from some of the labels on the x-axis, and is not aligned with any of the y-axis labels.
This will probably be easier to control with abline:
abline(v=x_axis_labels, h=y_axis_labels, lty=2, col='lightgray')
If you want the gridlines behind points etc., then try the panel.first argument to plot:
plot(as.matrix(d1[2,]), as.matrix(d2[2,]), type="o", col="red",
ann=FALSE, pch=17, log = 'y',lty=4, axes=FALSE, las=2,
panel.first=abline(v=x_axis_labels, h=y_axis_labels, lty=2, col='lightgray'))
Related
I used plot.new to combine two different graphs on R with this code:
par(mar=c(4, 4, 3, 5))
plot(d1, col="grey", yaxt="n", xlab="", ylab = "", ylim(0, 1.5), type = "h", fill ="grey")
axis(4, at=seq(0,1.5, by=0.05), col="grey", col.axis="grey")
mtext("Fn_1", side=4, line=2.5, col="grey")
mtext("Sqrt Insolation", side=1, line=2.5, col="black")
par(new=TRUE)
plot(h, axes=FALSE, type = "l", xlab = "", ylab="")
axis(2, ylim=c(-0.10, 0.1), at=seq(-0.10, 0.1, by=0.05), col="black", col.axis="black") mtext("Fn_2", side=2, line=2.5, col="black")
This is my result
https://i.stack.imgur.com/umCWu.png
I want to have a y axis like ylim = c (-0.10,1.5) and adjust the scale (h curb is way too big with this scale ..)
OR two y axes like here, but align on 0 with the same scale.
I tried to change the criteria of my axes but they seem to adjust automatically to make sense with the minimum and maximum of my data. I want to have one y axis as ylim = c(-0.10,1.5) and adjust scale (h courb is way too large with this actual scale..)
Can someone help me ?
Thank you very much
I wish to produce a plot similar to this. However, I would like the solid line dividing these two windows to be dotted. I've searched around the internet a bit but I still havent found anything useful. Any ideas would be highly appreciated.
layout(matrix(1:2,ncol=1),widths=1,heights=c(2,2),respect=FALSE)
par(mar = rep(0, 4), oma=c(4, 4, 4, 2), las=1)
plot(rnorm(100), type='l', ann=FALSE, xaxt='n')
plot(rnorm(100), type='l', ann=FALSE)
title("Hi", outer=TRUE)
mtext("x-axis", 1, 3, outer=TRUE)
mtext("y-axis", 2, 3, outer=TRUE, las=0)
You could over-write the upper box border of the lower plot with one of these:
abline(h= par("usr")[4], lty=3,col="white",xpd=TRUE, lwd=2)
# there is some bleed-through so to get a definite black-white dotted line needed to repeat the graphics call
corners=par('usr')
replicate(3, segments(x0= corners[1], x1= corners[2],
y0= corners[4], y1= corners[4],
lty=3,col="white",xpd=TRUE, lwd=2) )
Nuts. The png() output is different than the output on the interactive device (quartz()).
Little workaround. Need to figure out where exactly you overplot the border. Would just go with something like this:
set.seed(1234)
par(lty=1)
layout(matrix(1:2,ncol=1),widths=1,heights=c(2,2),respect=FALSE)
par(mar = rep(0, 4), oma=c(4, 4, 4, 2), las=1)
plot(rnorm(100), type='l', ann=FALSE, xaxt='n')
plot(rnorm(100), type='l', ann=FALSE)
par(lty=2)
abline(h=3.27, col="white")
par(lty=1)
I am trying to generate a figure that consists of a box plot with a set of points overlaid on the boxplot. The key issue is that the y scale of the box plot is different from that of the points. (Yes, this is very poor visualization - but I'm not the lead author of the paper). I have been able to generate a plot with different y scales, but am facing an issue with the x axis.
Using the following code
boxdata <- data.frame(fc=runif(100, min=-4, max=4),
sym=sample(c('A', 'B', 'C', 'D', 'E'), 100, replace=TRUE))
par(mar=c(5, 4, 1, 6) + 0.1)
junk <- boxplot(fc ~ sym, boxdata, las=2, pch=19, ylim=c(-5,5),
varwidth=FALSE, xaxt='n')
mtext("Y-axis",side=2,line=2.5)
axis(1, at=1:5, labels=sort(unique(boxdata$sym)), las=2)
par(new=TRUE)
x <- 1:5
y <- runif(5, min=-1, max=1)
plot(x,y, col='red', type='p', pch=15, axes=FALSE, ylim=c(-1,1), cex=1.5)
axis(4, ylim=c(-1,1), las=1)
I get the following figure. As you can see the points in red do not align with the X-axis labels (or box centers). The box centers are located at 1:5, so I thought that the plot() call with x = 1:5 should line up.
Could anybody point me to a way to line up the second set of points with the box centers?
EDIT: This problem doesn't occur if I plot two sets of points on different y scales
plot(1:10, runif(10) , col='red', pch=19)
par(new=TRUE)
plot(1:10, runif(10, min=5, max=20), col='blue', pch=19, axes=FALSE)
axis(4, las=2)
Don't use par(new=TRUE), but use pointsinstead of the second plotcommand:
boxdata <- data.frame(fc=runif(100, min=-4, max=4),
sym=sample(c('A', 'B', 'C', 'D', 'E'), 100, replace=TRUE))
par(mar=c(5, 4, 1, 6) + 0.1)
junk <- boxplot(fc ~ sym, boxdata, las=2, pch=19, ylim=c(-5,5),
varwidth=FALSE, xaxt='n')
mtext("Y-axis",side=2,line=2.5)
axis(1, at=1:5, labels=sort(unique(boxdata$sym)), las=2)
x <- 1:5
y <- runif(5, min=-1, max=1)
points(x, 4*y, col='red', type='p', pch=15, ylim=c(-1,1), cex=1.5)
axis(4, at=seq(-4, 4, by=2), label=seq(-1, 1, by=.5), las=1)
EDIT: Check the ?bxp help page. You will find a note that xlim defaults to range(at, *) + c(-0.5, 0.5). So, you could specify the same for your second plot:
junk <- boxplot(fc ~ sym, boxdata, las=2, pch=19, ylim=c(-5,5),
varwidth=FALSE, xaxt='n')
mtext("Y-axis",side=2,line=2.5)
axis(1, at=1:5, labels=sort(unique(boxdata$sym)), las=2)
par(new=TRUE)
plot(x,y, col='red', type='p', pch=15, axes=FALSE, ylim=c(-1,1), cex=1.5,
xlim=range(x) + c(-0.5, 0.5))
axis(4, ylim=c(-1,1), las=1)
I need a two y-axes figure. hrbrmstr suggested to use simple plots. But when adapting the graph to my setting I observed I cannot add the ylab on the right hand side, getting a wired error:
Error in axis(4, ylim = c(0, 1), col = "black", col.axis = "black", las = 1, :
'labels' is supplied and not 'at'
Is this avoidable?
look at the code the bottom line fpr SOURCE OF ERROR
featPerf <- data.frame( expS=c("1", "2", "3", "4"),
exp1=c(1000, 0, 0, 0),
exp2=c(1000, 5000, 0, 0),
exp3=c(1000, 5000, 10000, 0),
exp4=c(1000, 5000, 10000,20000),
accuracy=c(0.4, 0.5, 0.65, 0.9) )
# make room for both axes ; adjust as necessary
par(mar=c(5, 5, 5, 7) + 0.2)
# plot the bars first with no annotations and specify limits for y
#barplot(as.matrix(featPerf[,2:5]), axes=FALSE, xlab="", ylab="", ylim=c(0, max(colSums(featPerf[2:5]))))
barplot(as.matrix(featPerf[,2:5]), axes=FALSE, xlab="", ylab="", beside=TRUE)
# make the bounding box (or not...it might not make sense for your plot)
#box()
# now make the left axis
axis(2, ylim=c(0, max(colSums(featPerf[2:5]))), col="black", las=1)
# start a new plot
par(new=TRUE)
# plot the line; adjust lwd as necessary
plot(x=1:4, y=featPerf[,6], xlab="Experiments", ylab="Abs. # of Features", axes=FALSE, type="l", ylim=c(0,1), lwd=5)
# annotate the second axis -- SOURCE OF ERROR -> VVVVVVVVVVVVVVVVVV
axis(4, ylim=c(0,1), col="black", col.axis="black", las=1, labels="Accuracy")
Like this?
par(mar=c(4,4,1,4) + 0.2)
barplot(as.matrix(featPerf[,2:5]), axes=FALSE, xlab="", ylab="", beside=TRUE)
axis(2, ylim=c(0, max(colSums(featPerf[2:5]))), col="black", las=1)
par(new=TRUE)
plot(x=1:4, y=featPerf[,6], xlab="Experiments", ylab="Abs. # of Features", axes=FALSE, type="l", ylim=c(0,1), lwd=5, col="blue")
axis(4, ylim=c(0,1), col="blue", col.axis="blue", las=1)
mtext("Accuracy",4,line=2, col="blue")
For the record, it is never a good idea to stack plots on top of each other this way (with two axes). I've made the line and the axis the same color in an attempt to draw attention to what you are doing, but this is still a very bad idea.
First of all it is not advisable to use two Y-axes in a same plot.
If you add at argument to the axis call, you get the name "Accuracy" on the right hand side of the plot.
axis(4, ylim=c(0,1), col="black", col.axis="black", las=1, labels="Accuracy",
at = .5)
I am trying to create a plot that shows two different time scales on the x-axis. The problem is that the two time scales have a complicated relationship.
I would like to show weather data by the day of year and by the thermal units. Thermal units are the accumulation of the mean temperatures of each day. Some days we get a lot of thermal units, some days not so many. I fit a spline to the relationship between day of year and thermal units and used that to predict thermal unit values for each day. So I do have a nice dataset with the following headers: day of year (day), thermal units (gdd), temperature (temp), precipitation (precip).
I created the following figure (may have to open in new window):
with this code:
pdf(file="Climate 2010.pdf", family="Times")
par(mar = c(5,4,4,4) + 0.3)
plot(cobs10$day, cobs10$precip, col="white", type="h", yaxt="n", xaxt="n", ylab="",
xlab="")
axis(side=3, col="black", labels=FALSE)
at = axTicks(3)
mtext(side = 3, text = at, at = at, col="black", line = 1, las=0)
mtext("Day of Year", side=3, las=0, line = 3)
par(new=TRUE)
plot(cobs10$gdd, cobs10$temp, type="l", col="red", yaxt="n", ylab="", xlab="Thermal
Units")
axis(side=2, col='red', labels=FALSE)
at= axTicks(2)
mtext(side=2, text= at, at = at, col = "red", line = 1, las=0)
mtext("Temperature (C)", side=2, las=0, line=3)
par(new=TRUE)
plot(cobs10$gdd, cobs10$precip, type="h", col="blue", yaxt="n", xaxt="n", ylab="",
xlab="")
axis(side=4, col='blue', labels=FALSE)
at = axTicks(4)
mtext(side = 4, text = at, at = at, col = "blue", line = 1,las=0)
mtext("Precipitation (cm)", side=4, las=0, line = 3)
dev.off()
This is exactly what I want, but I realized the x-axis scales are linear here, and they should not be. I put the top x-axis in by making my precipitation data white and writing over it. See what happens when I make it green:
It's obvious things don't match up. So how can I make the two axes in scale with eachother?
Here's the little dataframe I have been using where the time units are matched up by predicting:
cobs10.txt. "gdd" is thermal units
EDIT: Here is some new code that doesn't use par(new=TRUE):
par(mar = c(5,4,4,4) + 0.3)
plot(cobs10$gdd, cobs10$temp, type="l", col="red", yaxt="n", xlab="", ylab="",
ylim=c(-25, 30))
lines(cobs10$gdd, cobs10$precip, type="h", col="blue", yaxt="n", xlab="", ylab="")
axis(side=3, col="black", at=cobs10$gdd, labels=cobs10$day)
want<-(c(1, 130, 150, 170, 190, 210, 230, 250, 270, 360))
mtext(side = 3, text = want, at = want, col="black", line = 1, las=0)
mtext("Day of Year", side=3, las=0, line = 3)
axis(side=2, col='red', labels=FALSE)
at= axTicks(2)
mtext(side=2, text= at, at = at, col = "red", line = 1, las=0)
mtext("Temperature (C)", side=2, las=0, line=3)
axis(side=4, col='blue', labels=FALSE)
at = axTicks(4)
mtext(side = 4, text = at, at = at, col = "blue", line = 1,las=0)
mtext("Precipitation (cm)", side=4, las=0, line = 3)
It is almost never a good idea to use par(new=TRUE), it causes more problems than it solves.
You should decide which x axis units you want to use, days or thermal units and create the initial graph using that unit, then use functions like points or lines to add any additional points or lines to the existing graph using the existing units. You can then use the axis function to add another axis, use the original units for the at argument, but then the conversion to the other units for the labels (you need to decide if you want the locations of the ticks to match the original units, or be in locations that give pretty values for the converted units).