In order to generate a layout with multiple plots, I have the following code with some dummy plots:
jpeg("/path/to/file",height=10000,width=5000)
plot.new()
par(mar=c(2,2,1,1), oma=c(2,4,0,0), xpd=NA)
for (i in 1:10) {
par(mar=c(2,2,1,1),fig=c(0, 0.5, (10-i)/10, (11-i)/10), new=T)
matplot(rnorm(20)*sample(100,1),
col="blue",axes=F,type="l",lwd=10, xlab="",ylab="")
par(mar=c(2,2,1,1),fig=c(0.5, 1, (10-i)/10, (11-i)/10), new=T)
matplot(rnorm(20)*sample(100,1),
col="red",axes=F,type="l",lwd=10, xlab="",ylab="")
}
dev.off()
I want to add a vertical line/axis on the far LHS and the far RHS that span all 10 plots in a column. Since I will use this line as an axis, I need to be able to add ticks and labels.
You could draw axis by ?axis or ?Axis. To span your axis on multiple plots you have to reset the usr coordinates.
Please find a base graphics solution below:
## store number of rows
nRow <- 10
## your example code
## (only the number "10" is replaced by nRow and oma is adapted)
plot.new()
par(mar=c(2, 2, 1, 1), oma=c(2, 4, 0, 4), xpd=NA)
for (i in 1:nRow) {
par(mar=c(2, 2, 1, 1), fig=c(0, 0.5, (nRow-i)/nRow, ((nRow+1)-i)/nRow), new=TRUE)
matplot(rnorm(20)*sample(100, 1),
col="blue", axes=F, type="l", lwd=10, xlab="", ylab="")
par(mar=c(2, 2, 1, 1), fig=c(0.5, 1, (nRow-i)/nRow, ((nRow+1)-i)/nRow), new=TRUE)
matplot(rnorm(20)*sample(100, 1),
col="red", axes=F, type="l", lwd=10, xlab="", ylab="")
}
## define new user coordinates
usr <- c(0, 1, 0, 1) ## x1, x2, y1, y2
## calculate tick positons
## in general: (usr[3]+(diff(usr[3:4])/(nRow-1))*0:(nRow-1))
## but our usecase is much easier:
ticksAt <- 1/(nRow-1)*0:(nRow-1)
## choose left column and reset user plotting area (usr)
par(mar=c(2, 2, 1, 1), fig=c(0, 0.5, 0, 1), usr=usr, new=TRUE)
## draw axis; see ?Axis for details
Axis(side=2, at=ticksAt, labels=as.character(1:(nRow)), line=0.5)
## choose right column and reset user plotting area (usr, not needed because already done)
par(mar=c(2, 2, 1, 1), fig=c(0.5, 1, 0, 1), usr=usr, new=TRUE)
## draw axis; see ?Axis for details
Axis(side=4, at=ticksAt, labels=as.character((nRow+1):(2*nRow)), line=0.5)
You could make one overall plot of the entire device, add the axes there, then use the subplot function (TeachingDemos package) to do the plots within the large plot.
Related
I need to add a "separating" line in Base R boxplot to separate difference groups. In the example below, I want to separate groups A and B (each having 2 levels) using a horizontal line (in red). R codes for reproducible results:
dat = data.frame(A1 = rnorm(1000, 0, 1), A2 = rnorm(1000, 1, 2),
B1 = rnorm(1000, 0.5, 0.5), B2 = rnorm(1000, 1.5, 1.5))
boxplot(dat, horizontal = T, outline=F)
Is there an easy way to do in Base R?
Also, is there an easy way to color the y-axis labels? I want to have A1 and B1 shown as red, and A2 and B2 shown as blue in the axis.
Thanks!
Use abline. To get the right position take the mean of the axTicks of the y-axis.
To get the colored labels, first omit yaxt and rebuild axis ticks and mtext, also using axTicks.
b <- boxplot(dat, horizontal=T, outline=F, yaxt="n")
ats <- axTicks(2)
axis(2, labels=F)
mtext(b$names, 2, 1, col=c(2, 4), at=ats)
abline(h=mean(ats), lwd=2, col=2)
If you want axis tick label colors corresponding to the labels, use segments instead.
b <- boxplot(dat, horizontal=T, outline=F, yaxt="n")
ats <- axTicks(2)
abline(h=mean(ats), lwd=2, col=2)
pu <- par()$usr
Map(function(x, y) segments(pu[1] - .2, x, pu[1], x, xpd=T, col=y), ats, c(2, 4))
mtext(b$names, 2, 1, col=c(2, 4), at=ats)
Edit: To adjust the space a little more use at=option in boxplot and leave out the middle axTicks.
b <- boxplot(dat, horizontal=T, outline=F, yaxt="n", at=c(1, 2, 4, 5))
ats <- axTicks(2)[-3]
abline(h=mean(ats), lwd=2, col=2)
pu <- par()$usr
Map(function(x, y) segments(pu[1] - .2, x, pu[1], x, xpd=T, col=y), ats, c(2, 4))
mtext(b$names, 2, 1, col=c(2, 4), at=ats)
For the two column data available here, I am plotting two logarithmic y-axis histograms in one diagram in RStudio:
data = read.table("C:\\test\\test.csv", header=TRUE, sep=",")
par( mar=c(3.1, 5.1, 0, 0))
hist.x <- hist(data$a, plot = FALSE, breaks=50)
hist.x$counts <- log10(hist.x$counts + 1)
plot(hist.x, col = rgb(0, 0, 1, 0.99), main="", xlab="", ylab="", yaxt="n")
yAxesTitles=c(1, 10, 100, 1000, 10000)
axis(2, at=c(0, 1, 2, 3, 4),labels=yAxesTitles, col.axis="black", las=2)
mtext(side = 3, text = "a vs b", line = 0, cex=1.3)
mtext(side = 1, text = "Number", line = 2)
mtext(side = 2, text = "Frequency", line = 4)
# Adding the second diagram to the first one:
relocatedData=data$b+0.2
hist.y <- hist(relocatedData, plot = FALSE, breaks=50)
hist.y$counts <- log10(hist.y$counts + 1)
plot(hist.y, col = rgb(1, 0, 0, 0.99), main="", xlab="", ylab="", yaxt="n", add=TRUE)
legend(7.5, 4, c("a", "b"), lwd=c(1, 1), col=c(rgb(0, 0, 1, 0.99), rgb(1, 0, 0, 0.99)), pch = c(15, 15), pt.cex=2)
And this is what I have till now:
Now, there are two problems in this plot:
1- I want to add texture to the red bars (or two different patterns
for red and blue). I tried the regular texture solutions but couldn't successfully apply them in my specific diagram.
2- The space between the first bars (at 0) and the next bars (at 1) is less than other spaces (e.g., between 1 and 2, between 2 and 3 and so on). It seems that it automatically centered any two bars at each of the ticks except at 0 (which it puts both to the right side of zero).
Any solutions?
I have this plot which I want to save as PDF.
pdf(file="pie_charts.pdf", width=8, height=5, onefile=F)
layout(matrix(c(1,2,3,3), ncol=2, byrow=TRUE), heights=c(4, 1))
par(mar=c(0,0,0,0), xpd=TRUE)
pie(c(1,9),col=c("black","white"))
pie(c(1,3),col=c("black","white"))
plot.new()
legend(x="center", ncol=2,legend=c("Black","Whtie"),fill=c("black","white"), bty = "n",cex=1.3)
dev.off()
And this is what I am getting
It looks quite good but I want to eliminate as much empty space as possible between the individual pie charts as well as between them and the legend. Any suggestions?
With layout(), I think you may be a bit limited with changing margins to squeeze the pie charts together.
This isn't an elegant solution but it works. I went in to the pie() function and modified the xlim arguments. This was my only change.
In other words, pie has this inside its function:
xlim <- ylim <- c(-1, 1)
Change the xlim to shift the pie charts left or right.
I made mypieleft() and mypieright().
mypieleft<-function(blah blah){
[untouched code from pie]
# xlim <- ylim <- c(-1, 1)
xlim <- c(-1.20, 0.80)
ylim <- c(-1, 1)
[untouched code from pie]
}
and
mypieright<-function(blah blah){
[untouched code from pie]
# xlim <- ylim <- c(-1, 1)
xlim <- c(-0.75, 1.25)
ylim <- c(-1, 1)
[untouched code from pie]
}
Then change your code slightly:
layout(matrix(c(1,2,3,3), ncol=2, byrow=TRUE), heights=c(4, 1))
par(oma=c(0,0,0,0), xpd=TRUE)
mypieleft(c(1,9),col=c("black","white"))
mypieright(c(1,3),col=c("black","white"))
plot.new()
legend(x="center", ncol=2,legend=c("Black","Whtie"),fill=c("black","white"), bty = "n",cex=1.3)
I get this image.
Just increase the radius of the pies:
layout(matrix(c(1, 2, 3, 3), ncol=2, byrow=TRUE), heights=c(4, 1))
par(mar=c(0, 1, 0, 0)) # increase left margin to accommodate text
pie(c(1, 9), col=c("black","white"), radius=1)
par(mar=c(0, 0, 0, 1)) # increase right margin to accommodate text
pie(c(1, 3), col=c("black", "white"), radius=1)
plot.new()
legend(x="center", ncol=2, legend=c("Black", "White"),
fill=c("black", "white"), bty="n", cex=1.3)
See the radius arg at ?pie.
So i have this numeric variables which reflect percentages
data1.pct<-19
data2.pct<-5
data3.pct<-76
class1.pct<-35
class2.pct<-18
class3.pct<-47
Now i am using this code to generate barplot
CairoPDF(paste('data1/', data, '_plot1.pdf', sep=''), family='sans', pointsize=9, width=6, height=3.25)
par(mar=(c(4, 4, 1, 13) + 0.1), mgp=c(3, 2, 0), xpd=TRUE)
barplot(cbind(
c(data1.pct, data2.pct, data3.pct),
c(class1.pct, class2.pct, class3.pct)), col=c("firebrick3", "dodgerblue3", "mistyrose1"), ylim=c(0,100), space=c(0,1)
)
legend("topright", inset=c(-0.55, 0), legend=c("not attend", "refused", "attend"), col=c("mistyrose1", "dodgerblue3", "firebrick3"), lty=1, lwd=2, bty='n')
dev.off()
and the result is
I would like to add corresponding percentages inside barplot, that is numbers/percentages in my variables. So My output should be:
I would like to use barplot funcion to do this and NOT ggplot2
I have tried adding percentages with
text(mydata, 0, round(data1.pct), 1),cex=1,pos=3) but this is not right.
To get the y-values for the text, you can use cumsum along with tail and head to get the midpoints of each bar section.
par(mar=(c(4, 4, 1, 13) + 0.1), mgp=c(3, 2, 0), xpd=TRUE)
## Make the matrix for barplot
mat <- cbind(c(data1.pct, data2.pct, data3.pct), c(class1.pct, class2.pct, class3.pct))
## Get the y-values for text
ys <- apply(mat, 2, function(x) c(x[1]/2, head(cumsum(x),-1) + tail(x,-1)/2))
## Make barplot, store x data
xs <- barplot(mat, col=c("firebrick3", "dodgerblue3", "mistyrose1"), ylim=c(0,100), space=c(0,1))
## Add text
text(rep(xs, each=nrow(ys)), c(ys), labels=c(mat))
legend("topright", inset=c(-0.55, 0), legend=c("not attend", "refused", "attend"), col=c("mistyrose1", "dodgerblue3", "firebrick3"), lty=1, lwd=2, bty='n')
Hi everybody I have 3 plots with density bars on either axis which I have done this way (here is a simpler form presented with only 3 ordinary plots but the other parts are necessary as required for a more complicated function which I have left off here just for the ease of viewing)
scatterBar.Norm <- function(x,y) {
zones <- matrix(c(2,0,1,3), ncol=2, byrow=TRUE)
layout(zones, widths=c(5/7,2/7), heights=c(2/7,5/7))
title("My Title", outer=TRUE);
par(mar=c(3,3,1,1),mgp=c(2,1,0))
plot(1:10, xlab="Magnification", ylab="residue", col=2)
par(mar=c(0,3,1,1))
plot(1:10, xlab="Magnification", ylab="residue",col=3)
par(mar=c(3,0,1,1))
plot(1:10, xlab="Magnification", ylab="residue", col=4)}
scatterBar.Norm(2,3)
The problem :
Firstly the The plot title the "My Title" part is going out of the canvas , how to fix it ?
Thanks for the much needed help in advance.
You've instructed R to plot the title in the outer margin, but (at least in your example) you haven't set up that margin. The following should work:
scatterBar.Norm <- function(x, y) {
zones <- matrix(c(2, 0, 1, 3), ncol=2, byrow=TRUE)
layout(zones, widths=c(5, 2), heights=c(2, 5))
par(mar=c(3, 3, 1, 1), mgp=c(2, 1, 0), oma=c(0, 0, 3, 0))
plot(1:10, xlab="Magnification", ylab="residue", col=2)
par(mar=c(0, 3, 1, 1))
plot(1:10, xlab="Magnification", ylab="residue", col=3)
par(mar=c(3, 0, 1, 1))
plot(1:10, xlab="Magnification", ylab="residue", col=4)
title("My Title", outer=TRUE)
}
plot.new()
scatterBar.Norm(2, 3)