Superscript numbers in a forestplot

[lay]

I attempt to insert references in a forestplot and superscript the numbers. Here is part of my data and codes, the numbers[23], [22], [9], [21] in the first column is the inserted references:

			hr1	ci.lb1	ci.ub1	hr2	ci.lb2	ci.ub2
Author	HR(95%CI)
	LM	non-LM
Louis 2016[23]	0.64(0.37,1.1)	0.68(0.49,0.94)	0.64	0.37	1.1	0.68	0.49	0.94
Achim 2017[22]	0.82(0.59,1.14)	0.72(0.6,0.88)	0.82	0.59	1.14	0.72	0.6	0.88
Ramalingam et al 2019[9]	0.82(0.62,1.08)	0.72(0.62,0.85)	0.82	0.62	1.08	0.72	0.62	0.85
Cappuzzo et al 2019[21]	1.04(0.63,1.72)	0.73(0.57,0.92)	1.04	0.63	1.72	0.73	0.57	0.92
Borghaei et al 2020[24]	0.8(0.49,1.31)	0.61(0.48,0.79)	0.8	0.49	1.31	0.61	0.48	0.79
Reck M. et al 2021[8]	0.54(0.34,0.85)	0.83(0.65,1.06)	0.54	0.34	0.85	0.83	0.65	1.06
Reck M et al 2021[25]	0.83(0.57,1.2)	0.64(0.51,0.8)	0.83	0.57	1.2	0.64	0.51	0.8
Makoto et al 2021[19]	0.96(0.58,1.58)	0.86(0.69,1.06)	0.96	0.58	1.58	0.86	0.69	1.06
Pooled HR	0.80(0.70,0.92)	0.72(0.67,0.78)	0.8	0.7	0.92	0.72	0.67	0.78

forest<-read.delim("clipboard")

attach(forest)

labeltext <- as.matrix(forest[,1:3])

coef <- with(forest, cbind(hr1, hr2))

low <- with(forest, cbind(ci.lb1, ci.lb2))

high <- with(forest, cbind(ci.ub1, ci.ub2))

library(forestplot)

forestplot(labeltext, mean = coef, lower = low, upper = high, zero = 1, lwd.zero = 2,graph.pos = 2,boxsize = 0.25,align = "l", col=fpColors(box=c("#B30638", "#00549E")),lwd.xaxis=2)

What should I do?

[FJCC]

The last few posts in the following thread show how to store text in a data frame that can be used to display superscripts in a plot. Is that a solution to your problem? A data frame cannot store formatted text, as far as I know.

Superscript and Subscript character in R

How we can assign superscript and subscript in R. for example marklist<- c(98,74,32,58,64,98,85,51) names<- c("A","B","C","D","E","F","G","H") grade<-data.frame(marklist,names) library(tidyverse) grade <- grade %>% mutate(grade= if_else(marklist>=90, "A", if_else(marklist>=85, "B+",if_else(marklist>=75, "C", if_else(marklist>=50, "D","F"))))) print(grade) grade marklist names grade 1 98 A A 2 74 B D 3 32 C F 4 58 D D 5 64 E D 6 98 F A 7 85 G B+ 8 51 H D my question is how I can write B plus superscript as a character " B +" plus sign should be superscript.

[technocrat]

Due to the limitations of reprex the script will not render a^1 as the output, but it will appear in the RStudio viewer pane when copied and run.

library(katex)
library(stringr)

# create a data frame 
x <- c("a1", "b2")
y <- c("c3", "d4")
# avoid naming objects after built-in functions
# like c, df, data, etc. as an easy way of 
# avoiding namespace conflicts that can cause
# an error
# view it
dat <- data.frame(x, y)
# write a function to convert values to 
# superscripted versions for the case of
# a single lower-case letter with one or
# more integers in either order a1 or 1a
script_up <- function(x) {
  the_letter = "[a-z]"
  the_number = "[0-9]+"
  letter_part = str_extract(x,the_letter)
  number_part = str_extract(x,the_number)
  katex_html(paste0(letter_part,"^",number_part),include_css = TRUE)
}

script_up(dat[1,1])

a1a^1a1

[lay]

Thanks for your kindness. Actually i attempt to insert references in a forestplot and superscript the numbers. Now it seems better not to do this in a dataframe. Would you please be so kind to give me a solution? Here is part of my data and codes, the numbers[23], [22], [9], [21] in the first column is the inserted references:

			hr1	ci.lb1	ci.ub1	hr2	ci.lb2	ci.ub2
Author	HR(95%CI)
	LM	non-LM
Louis 2016[23]	0.64(0.37,1.1)	0.68(0.49,0.94)	0.64	0.37	1.1	0.68	0.49	0.94
Achim 2017[22]	0.82(0.59,1.14)	0.72(0.6,0.88)	0.82	0.59	1.14	0.72	0.6	0.88
Ramalingam et al 2019[9]	0.82(0.62,1.08)	0.72(0.62,0.85)	0.82	0.62	1.08	0.72	0.62	0.85
Cappuzzo et al 2019[21]	1.04(0.63,1.72)	0.73(0.57,0.92)	1.04	0.63	1.72	0.73	0.57	0.92

forest<-read.delim("clipboard")
attach(forest)

labeltext <- as.matrix(forest[,1:3])

coef <- with(forest, cbind(hr1, hr2))

low <- with(forest, cbind(ci.lb1, ci.lb2))

high <- with(forest, cbind(ci.ub1, ci.ub2))

library(forestplot)

forestplot(labeltext, mean = coef, lower = low, upper = high, zero = 1, lwd.zero = 2,graph.pos = 5,boxsize = 0.25,align = "l", hrzl_lines = list("2" = gpar(lty=1, columns=c(2:7), col = "black"), "3" = gpar(lty=1, columns=c(6:7), col = "black")),is.summary= c(T,T,F,F,F,F,F,F,F,F,F,F,F,F,F,T,F,F,F,F,F,F,F),col=fpColors(box=c("#B30638", "#00549E")),legend=c("LM", "non-LM"), legend_args = fpLegend(pos = list(x =3, y=-0.02),r = unit(.1, "snpc")),txt_gp = fpTxtGp(label = gpar(cex = 1.0,fontfamily="myFont1"),ticks = gpar(cex=1.20),xlab = gpar(cex=1.15)),xlab="<---favor intervention-- --favor control--->",lwd.xaxis=2)

[lay]

I really appreciate that.Actually i had read those posts and found they were not what i want. I attempt to insert references in a forestplot and superscript the numbers. Now it seems better not to do this in a dataframe. Would you please be so kind to give me a solution? Here is part of my data and codes, the numbers[23], [22], [9], [21] in the first column is the inserted references:

			hr1	ci.lb1	ci.ub1	hr2	ci.lb2	ci.ub2
Author	HR(95%CI)
	LM	non-LM
Louis 2016[23]	0.64(0.37,1.1)	0.68(0.49,0.94)	0.64	0.37	1.1	0.68	0.49	0.94
Achim 2017[22]	0.82(0.59,1.14)	0.72(0.6,0.88)	0.82	0.59	1.14	0.72	0.6	0.88
Ramalingam et al 2019[9]	0.82(0.62,1.08)	0.72(0.62,0.85)	0.82	0.62	1.08	0.72	0.62	0.85
Cappuzzo et al 2019[21]	1.04(0.63,1.72)	0.73(0.57,0.92)	1.04	0.63	1.72	0.73	0.57	0.92
Borghaei et al 2020[24]	0.8(0.49,1.31)	0.61(0.48,0.79)	0.8	0.49	1.31	0.61	0.48	0.79
Reck M. et al 2021[8]	0.54(0.34,0.85)	0.83(0.65,1.06)	0.54	0.34	0.85	0.83	0.65	1.06
Reck M et al 2021[25]	0.83(0.57,1.2)	0.64(0.51,0.8)	0.83	0.57	1.2	0.64	0.51	0.8
Makoto et al 2021[19]	0.96(0.58,1.58)	0.86(0.69,1.06)	0.96	0.58	1.58	0.86	0.69	1.06
Pooled HR	0.80(0.70,0.92)	0.72(0.67,0.78)	0.8	0.7	0.92	0.72	0.67	0.78

forest<-read.delim("clipboard")

[technocrat]

See the FAQ: How to do a minimal reproducible example reprex for beginners for the preferred way to providing representative data and code.

[lay]

Sorry about that , i've edited the data and codes on top.

[technocrat]

Please see the reprex FAQ--the point is to provide a complete script with enough data to illustrate the problem in a form that can be cut and pasted by the reader so a solution can be proposed and illustrated.

Here's an example

# library(dplyr) # not needed here, but use for any that are
my_matrix <- structure(c(
  NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
  NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
  NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
  NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
  NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
  NA, NA, NA, NA, NA, NA, NA
), .Dim = c(6L, 14L), .Dimnames = list(
  c("P18", "P19", "P20", "P21", "P22", "P23"), c(
    "P35_cor",
    "P35_p", "P36_cor", "P36_p", "P37_cor", "P37_p", "P38_cor",
    "P38_p", "P39_cor", "P39_p", "P40_cor", "P40_p", "P41_cor",
    "P41_p"
  )
))

# odd and even columns

# get indices of columns
get_index <- function(x,y) seq(from = y, to = dim(x)[2],by = 2)

my_matrix[,get_index(my_matrix,1)]
#>     P35_cor P36_cor P37_cor P38_cor P39_cor P40_cor P41_cor
#> P18      NA      NA      NA      NA      NA      NA      NA
#> P19      NA      NA      NA      NA      NA      NA      NA
#> P20      NA      NA      NA      NA      NA      NA      NA
#> P21      NA      NA      NA      NA      NA      NA      NA
#> P22      NA      NA      NA      NA      NA      NA      NA
#> P23      NA      NA      NA      NA      NA      NA      NA

my_matrix[,get_index(my_matrix,2)]
#>     P35_p P36_p P37_p P38_p P39_p P40_p P41_p
#> P18    NA    NA    NA    NA    NA    NA    NA
#> P19    NA    NA    NA    NA    NA    NA    NA
#> P20    NA    NA    NA    NA    NA    NA    NA
#> P21    NA    NA    NA    NA    NA    NA    NA
#> P22    NA    NA    NA    NA    NA    NA    NA
#> P23    NA    NA    NA    NA    NA    NA    NA

[lay]

forest<-structure(list(Author = c("Richard2012[1]", "Wang2015[2]"), coef = c(0.3, 0.45), low = c(0.1, 0.2), high = c(0.4, 0.55)), class = "data.frame", row.names = c(NA, -2L))
labeltext <- as.matrix(forest[,1])
library(forestplot)
#> 载入需要的程辑包：grid
#> 载入需要的程辑包：magrittr
#> 载入需要的程辑包：checkmate
forestplot(labeltext, mean = coef, lower = low, upper = high)
#> Error in NCOL(lower): 找不到对象'low'

^{Created on 2022-02-23 by the reprex package (v2.0.1)}
Sorry for the late reply . I clearly assigned values to low, yet there is always"Error: object 'low' can not be found". I was totally confused and asked many people without an answer.Is this data appropriate now?

[cderv]

Your variables are inside your forest object, so you need to pick them there. This works for me.

forest<-structure(list(Author = c("Richard2012[1]", "Wang2015[2]"), coef = c(0.3, 0.45), low = c(0.1, 0.2), high = c(0.4, 0.55)), class = "data.frame", row.names = c(NA, -2L))
labeltext <- as.matrix(forest[,1])
library(forestplot)
#> Le chargement a nécessité le package : grid
#> Le chargement a nécessité le package : magrittr
#> Le chargement a nécessité le package : checkmate
forestplot(labeltext, mean = forest$coef, lower = forest$low, upper = forest$high)

^{Created on 2022-03-04 by the reprex package (v2.0.1)}

[cderv]

If your question's been answered (even by you!), would you mind choosing a solution? It helps other people see which questions still need help, or find solutions if they have similar problems. Here’s how to do it:

FAQ: How do I mark a solution?

If your question has been answered, don't forget to mark the solution! How do I mark a solution? Find the reply you want to mark as the solution and look for the row of small gray icons at the bottom of that reply. Click the one that looks like a box with a checkmark in it: [image] Hovering over the mark solution button shows the label, "Select if this reply solves the problem". If you don't see the mark solution button, try clicking the three dots button ( ••• ) to expand the full set of options. When a solution is chosen, the icon turns green and the hover label changes to: "Unselect if this reply no longer solves the problem". Success! [solution_reply_author] …

[lay]

Sure.It turns out to be a stupid question.Thanks!