My example data is as follows:
df <- data.frame(study = c("Hodaie","Kerrigan","Lee","Andrade","Lim"), SR = c(0.5460, 0.2270, 0.7540, 0.6420, 0.5000), SE = c(12.30, 15.70, 12.80, 13.80, 9.00), Patients = c(5, 5, 3, 6, 4))
I want to conduct the meta-analysis with SR(single group percentage), SE (standard error that I can compute based on sample size and percentage), and patients(sample size for each study), and I hope I could get the following forest plot (I found this example in an article, and they also have one group percentage data, but I can't find which R statement or argument they used):
Could anyone tell me which R statement or argument that I could use to conduct the meta-analysis and generate the forest plot above? Thank you!
I am sure there are plenty of ways to do this using packages but it can be accomplished in base R (and there are likely more elegant solutions using base R). The way I do it is to first build a blank plot much larger than the needed graphing portion, then overlay the relevant elements on it. I find one has more control over it this way. A basic example that could get you started is below. If you are new to R (based on your name NewRUser), I suggest running it line-by-line to see how it all works. Again, this is only one way and there are likely better approaches. Good luck!
Sample Data
#### Sample Data (modified from OP)
df <- data.frame(Study = c("Hodaie","Kerrigan","Lee","Andrade","Lim"),
SR = c(0.5460, 0.2270, 0.7540, 0.6420, 0.5000),
SE = c(12.30, 15.70, 12.80, 13.80, 9.00),
Patients = c(5, 5, 3, 6, 4),
ci_lo = c(30, -8.0, 50, 37, 32),
ci_hi = c(78, 53, 100, 91, 67))
### Set up plotting elements
n.studies <- nrow(df)
yy <- n.studies:1
seqx <- seq(-100, 100, 50)
## blank plot much larger than needed
plot(range(-550, 200), range(0, n.studies), type = 'n', axes = F, xlab = '', ylab = '') #blank plot, much bigger than plotting portion needed
# Set up axes
axis(side = 1, at = seqx, labels = seqx, cex.axis = 1, mgp = c(2, 1.5, 1)) # add axis and label (bottom)
mtext(side = 1, at = 0, 'Seizure Reduction', line = 2.5, cex = 0.85, padj = 1)
axis(side = 3, at = seqx, labels = seqx, cex.axis = 1, mgp = c(2, 1.5, 1)) # add axis and label (top)
mtext(side = 3, at = 0, 'Seizure Reduction', line = 2.5, cex = 0.85, padj = -1)
## add lines and dots
segments(df[, "ci_lo"], yy, df[,"ci_hi"], yy) # add lines
points(df[,"SR"]*100, yy, pch = 19) # add points
segments(x0 = 0, y0 = max(yy), y1 = 0, lty = 3, lwd = 0.75) #vertical line # 0
### Add text information
par(xpd = TRUE)
text(x = -550, y = yy, df[,"Study"], pos = 4)
text(x = -450, y = yy, df[,"SR"]*100, pos = 4)
text(x = -350, y = yy, df[,"SE"], pos = 4)
text(x = -250, y = yy, df[,"Patients"], pos = 4)
text(x = 150, y = yy, paste0(df[,"ci_lo"], "-", df[,"ci_hi"]), pos = 4)
text(x = c(seq(-550, -250, 100), 150), y = max(yy)+0.75,
c(colnames(df)[1:4], "CI"), pos = 4, font = 2)
# Add legend
legend(x = 50, y = 0.5, c("Point estimate", "95% Confidence interval"),
pch = c(19, NA), lty = c(NA, 19), bty = "n", cex = 0.65)
I have the following code (Thanks to an answer from #Rawr in this question):
labes1 <- c("P(LNG)","","Volume(LNG)","","P(oil)","","Can.GDP","","US GDP","")
titles <- c("Levels","","","","","Log Difference","","","","")
par(mfrow = c(5, 2), mar = c(0.3, 6, 0, 2), oma = c(5, 0, 3, 2))
lapply(1:10, function(ii) {
x <- plotdata1[, ii, drop = FALSE]
plot(x, xlab = "Quarter", ylab = labes1[ii], axes = FALSE)
axis(2, las = 1)
box()
if (ii %in% 9:10) {
axis(1)
title(xlab = 'Quarter', xpd = NA)
}
if (ii %in% 1:2)
title(main = c('Levels', 'Log Difference')[ii], xpd = NA, line = 1)
})
This produces the following plot:
The obvious issue is the overlaying of the y-axis labels with the y-axis values. I have tried playing around with the mar() and oma() but these just change the margins around, I was hoping this would move things out of the way. How can I move the y-axis labels as separate from the plot? I will also be moving the margins a bit so that the white space between the two columns of plots will be closer together.
You can define the ylab separately, like what you're doing for the xlab, and set the line parameter to define its distance from the plot (as stated in this post).
I got a running example from combining your code and #rawr's from your previous question.
set.seed(1)
z <- ts(matrix(rt(200 * 10, df = 3), 200, 10), start = c(1961, 1), frequency = 12)
z <- z * 1e5 # to make "wide" y-axis labels
## vectors of x, y, and main labels
xl <- sprintf('x label %s', 1:10)
yl <- sprintf('y label %s', 1:10)
ml <- sprintf('main label %s', 1:10)
labes1 <- c("P(LNG)","","Volume(LNG)","","P(oil)","","Can.GDP","","US GDP","")
titles <- c("Levels","","","","","Log Difference","","","","")
par(mfrow = c(5, 2), mar = c(0.3, 6, 0, 2), oma = c(5, 0, 3, 2))
lapply(1:10, function(ii) {
x <- z[, ii, drop = FALSE]
plot(x, xlab = "Quarter", ylab = "", axes = FALSE) # set ylab to ""
axis(2, las = 1)
title(ylab = labes1[ii], line = 4) # set the line at an appropriate distance
box()
if (ii %in% 9:10) {
axis(1)
title(xlab = 'Quarter', xpd = NA)
}
if (ii %in% 1:2)
title(main = c('Levels', 'Log Difference')[ii], xpd = NA, line = 1)
})
The code above outputs the following graph for line = 4 :
and this plot for line = 3 :
I'm trying to make a plot with specific axes, while keeping the aspect ratio as 1.
the problem is there is parts of the plot that i don't need and want to remove.
I can manage it using margin:
## Creating Data
x <- seq(1, 100, length.out = 100)
y <- seq(1, 400, length.out = 100)
## Playing with margins
par(fin = c(3.75, 5.3) , mar = c(2, 9, 1, 3) + 0.1 )
## Making
plot(y ~ x ,asp = 1)
abline(v = -10)
abline(v = 120)
But if i want to plot multiple plots i dont know how to remove it
## Using mfrow
par(mfrow = c(3,2))
for (i in 1:6) {
plot(y ~ x ,asp = 1,xlim = c(0,100), ylim = c(0,400))
abline(v = -10)
abline(v = 120)
}
How can i do it for the multiple plots?
This might be closer, using the layout method (see this question and layout R documentation):
x <- seq(1, 100, length.out = 100)
y <- seq(1, 400, length.out = 100)
plot.new()
par(mai = c(0.6,0.5,0.3,0.3))
layout(matrix(c(1,2,3,4,5,6), nrow = 2, ncol = 3, byrow = TRUE))
for (i in 1:6) {
plot(y ~ x ,asp = 1, ylim = c(0,400))
abline(v = -10)
abline(v = 120)
}
The par(mai=c(b,l,t,r)) option changes the size of the whitespace surrounding the subplots.
I have written the following code below. I would like to overlay a bar graph with a line graph. The code I have does it all but with just one problem. I would like the points on the line graph to be in the center of the bar graph, i.e. they should shift to the left a little bit. where Im I missing it? If this can be done in ggplot as well I would be happy too. but even base r would do
par(mai = c ( 1 , 2, 1, 1), omi = c(0, 0, 0, 0))
yy <- c(31,31,31,50,50,61,69,75,80,88,94,101,108,115,121,124,125,125,125,126,127)
name1 <- c ("15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35")
xx <- barplot(yy, ylab = "", names.arg = name1, ylim = c(0, 140),col="steelblue")
text(xx, yy + 3, labels = as.character(yy),srt=45)
mtext(2,text="",line=2)
par(new = T)
xx2 <- c(15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35)
yy2 <- c(379,474,579,725,922,1181,1473,1846,2316,2962,3688,4786,6069,7605,9504,10680,11074,11074,11074,11483,11484)
plot(xx2, yy2, xlim = c(14, 36), ylim = c(0, 14000),type ="n" , axes = F, xlab ="", ylab ="",col="blue",main="")
lines(xx2, yy2, lwd = 2,col="red",lty=1)
points(xx2, yy2, pch = 18, cex = 1,col="red")
text(xx2, yy2 + 4 , labels = as.character(yy2),srt=90)
par(new = T)
par(mai = c ( 1 , 1, 1, 1))
axis(2)
mtext(2,text="",line=2.5)
mtext("",side=1,col="black",line=2)
grid()
It can be quote tricky to get things to line up if you use barplot and a standard plot(). I recommend only calling plot once. In order to do this, you will need to rescale your yy2 values to the same scale as yy. Here's how you might do that
par(mai = c ( 1 , 2, 1, 1), omi = c(0, 0, 0, 0))
yy <- c(31,31,31,50,50,61,69,75,80,88,94,101,108,115,121,124,125,125,125,126,127)
name1 <- c ("15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35")
#draw bar plot
xx <- barplot(yy, ylab = "", names.arg = name1, ylim = c(0, 140),col="steelblue")
text(xx, yy + 3, labels = as.character(yy),srt=45)
mtext(2,text="",line=2)
xx2 <- xx #c(15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35)
yy2 <- c(379,474,579,725,922,1181,1473,1846,2316,2962,3688,4786,6069,7605,9504,10680,11074,11074,11074,11483,11484)
#transform data
yy2tx <- yy2/14000 * max(pretty(yy))
#draw line data
lines(xx2, yy2tx, lwd = 2,col="red",lty=1)
points(xx2, yy2tx, pch = 18, cex = 1,col="red")
text(xx2, yy2tx, labels = as.character(yy2),srt=90)
#draw axis for transformed data
par(mai = c ( 1 , 1, 1, 1))
axis(2, at=pretty(c(0,14000))/14000*max(pretty(yy)), labels=pretty(c(0,14000)))
grid()
This produces the following plot
The problem is that you have different x scale due to the different margins of the two plots.
Unless you want to find xx2 by hand... another solution to consider is to use a right y axis instead.
yy <- c(31,31,31,50,50,61,69,75,80,88,94,101,108,115,121,124,125,125,125,126,127)
name1 <- c ("15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35")
xx <- barplot(yy, ylab = "", names.arg = name1, ylim = c(0, 140),col="steelblue")
text(xx, yy + 3, labels = as.character(yy),srt=45)
mtext(2,text="",line=2)
par(new = T)
yy2 <- c(379,474,579,725,922,1181,1473,1846,2316,2962,3688,4786,6069,7605,9504,10680,11074,11074,11074,11483,11484)
plot(xx+0.5, yy2, "l", lwd = 2,col="red",lty=1,
axes=F, ylim=c(0, 14000), xlim=c(min(xx), max(xx)+1))
points(xx+0.5, yy2, pch = 18, cex = 1,col="red")
axis(4)
text(xx+0.5, yy2 + 4 , labels = as.character(yy2),srt=90)