text() function and x, y coordinates

[Andrzej]

Hi, I would like to understand how does it work I mean x, y coordinates in
text() function for base R plots. So what are reference points for x and y, where does it start ?
Is it somehow connected to x and y limits ?
Is it possible to draw like a grid like lines on the plot to temporarily show how to position text annotations precisely ?
thank you

[FJCC]

My quick test suggests that each text value is plotted with its center on the x,y coordinates.

X <- c(2,3,4,5)
Y <- c(23,25,27,29)
plot(X,Y)
text(X,Y,labels=c("AAAA","BBBB","CCCC","DDDD"))

There are arguments for adjusting this that are explained in the help file. What specific problem are you facing?

[Andrzej]

Thank you FJCC,

@FJCC

What specific problem are you facing?

I try to properly position elements in forest plot from Metafor package, and this is why I would like to understand how does it work I mean x, y coordinates in text() function from base R plots, especially, because I believe they are used in Metafor package in forest() plot function.
Here below, there is a sample code:

library(metafor)
library(readr)

dat  <-  readr::read_csv("https://stat.ethz.ch/pipermail/r-sig-meta-analysis/attachments/20180730/e790230b/attachment-0001.obj")

sub <- subset(dat, outcome=="periorneomortalityany" & Parity=="nullip" & Integration=="integ")

primary <- rma(yi, vi, data=sub, measure="OR", 
               slab = paste(sub$author, sub$year, sep=", "), 
               digits=2, level=95)

forest(primary, addfit=TRUE, showweights=TRUE, atransf=exp, 
       xlab="Odds Ratio", mlab="Random Effects Model", 
       order=order(sub$PragIdeal), 
       ilab=cbind(sub$HomePos, sub$HomeNeg, sub$HospPos, sub$HospNeg),
       ilab.xpos=c(-14.5,-12,-9,-6))

forest(primary, addfit=TRUE, showweights=TRUE, atransf=exp, 
       xlab="Odds Ratio", mlab="Random Effects Model", 
       order=order(sub$PragIdeal), 
       ilab=cbind(sub$HomePos, sub$HomeNeg, sub$HospPos, sub$HospNeg),
       ilab.xpos=c(-20,-16,-12,-8), xlim=c(-35,20), at=log(c(.01, .1, 1, 10, 100)))

So my question is, where is it :

 ilab.xpos=c(-14.5,-12,-9,-6))
 ilab.xpos=c(-20,-16,-12,-8)

Is it related to:

 xlim=c(-35,20)

Another example:
https://www.metafor-project.org/doku.php/plots:forest_plot_with_subgroups

### add additional column headings to the plot
text(c(-9.5,-8,-6,-4.5), 26, c("TB+", "TB-", "TB+", "TB-"))
text(c(-8.75,-5.25),     27, c("Vaccinated", "Control"))
 

### add text for the subgroups
text(-16, c(24,16,5), pos=4, c("Systematic Allocation",
                               "Random Allocation",
                               "Alternate Allocation"))

So I would like to know where is it on this plot:

text(c(-9.5,-8,-6,-4.5), 26,

text(-16, c(24,16,5), pos=4,

Please forgive me as somehow I don't see it yet.

[FJCC]

I am not familiar with the metafor package but the positioning of the text does seem to follow the usual logic. I suggest you start with this example:

@Andrzej

forest(primary, addfit=TRUE, showweights=TRUE, atransf=exp, 
       xlab="Odds Ratio", mlab="Random Effects Model", 
       order=order(sub$PragIdeal), 
       ilab=cbind(sub$HomePos, sub$HomeNeg, sub$HospPos, sub$HospNeg),
       ilab.xpos=c(-20,-16,-12,-8), xlim=c(-35,20), at=log(c(.01, .1, 1, 10, 100)))

remove the ilab, ilab.xpos, and xlim arguments and plot that. Then run

par("usr")[1:2]

That will display the x axis limits used for the plot. Then run forest() again but add in the argument xlim = c(-35,20) and see how the plot changes. Then add ilab=sub$HomePos and ilab.xpos=-20. You can repeat the plot with ilab.pos set to -16 and see how the text column moves. I think that will help clarify how the text is placed.
I do not understand how to pick the particular ilab.xpos values other than trial and error. However, I have never used the package, so I my understanding may be completely wrong.