I'm new to R and making a forestplot for a meta-analysis and need to add a superscript after the Author/Year on the left side of the graph. I have tried various methods to get the superscript added but keep getting error. e.g. when I try to use the expression function it states that forestplot cannot accept any expression values. Ideally I would like to use column names for both the author/year as well as the reference number to be superscripted, but I would be happy to just type them out at this point if it would work.
Basically in my dataframe "m" I have a column for the authors and years "fulltitle" as char (I wrote them out here in the hopes that expression would work), another column "refnum" that contains the reference number to be superscripted, and then the numeric data for the actual graph which is the mean and upper/lower CIs. If I use the studies without list(expression()) then it will work fine but I won't have any superscript after the title/year.
#Non-functioning code that gives error in bind_rows or !is_expression
#I'm using lattice as I am making another table with 112 studies that would not display otherwise
library(lattice)
trellis.device(device="windows", height = 4, width = 10, color=TRUE)
base_data <- tibble(mean = (m$overall_survival_mean_of_months),
lower = (m$CILower),
upper = (m$CIUpper),
study = list(expression("N 2000"^2),
expression("S 1992"^1),
expression("K 2012"^1),
expression("S 2013"^1),
expression("A 2012"^1),
expression("S 2005"^1),
expression("M 2001"^1),
expression("B 1993"^1),
expression("B 2017"^1),
expression("H 2013"^1),
expression("L 2017"^1),
expression("S 2018"^1)),
sample_size = as.character(m$number_of_patients),
OS = as.character(m$overall_survival_mean_of_months))
summary <- tibble(mean = 6,
lower = 2,
upper = 10,
study = expression("Studies"),
sample_size = "1,000 patients (12 studies)",
OS = "6.0 ± 4.0 months",
summary = TRUE)
header <- tibble(study = c(expression("", "Study")),
sample_size = c("", "Number of Patients"),
OS = c("", "Overall Survival"),
summary = TRUE) empty_row <- tibble(mean = NA_real_)
cochrane_output_df <- bind_rows(header,
base_data,
empty_row,
summary)
cochrane_output_df %>%
forestplot(labeltext = c(study, sample_size, OS),
is.summary = summary,
clip = c(0,40),
exp = FALSE,
colgap = unit(4,"mm"),
xlog = FALSE,
txt_gp = fpTxtGp(cex = 0.5),
col = fpColors(box = "royalblue",
line = "darkblue",
summary = "royalblue"))
#Error in if (!is.expression(row_column_text) && !is.call(row_column_text) && : missing value where TRUE/FALSE needed
Working code (without superscripts)
base_data <- tibble(mean = (m$overall_survival_mean_of_months),
lower = (m$CILower),
upper = (m$CIUpper),
study = c(as.character(("N 2000"),
("S 1992"),
("K 2012"),
("S 2013"),
("A 2012"),
("S 2005"),
("M 2001"),
("B 1993"),
("B 2017"),
("H 2013"),
("L 2017"),
("S 2018"))),
sample_size = as.character(m$number_of_patients),
OS = as.character(m$overall_survival_mean_of_months))
summary <- tibble(mean = 6,
lower = 2,
upper = 10,
study = "Studies",
sample_size = "1,000 patients (12 studies)",
OS = "6.0 ± 4.0 months",
summary = TRUE)
header <- tibble(study = c("", "Study"),
sample_size = c("", "Number of Patients"),
OS = c("", "Overall Survival"),
summary = TRUE)
empty_row <- tibble(mean = NA_real_)
cochrane_output_df <- bind_rows(header,
base_data,
empty_row,
summary)
cochrane_output_df %>%
forestplot(labeltext = c(study, sample_size, OS),
is.summary = summary,
clip = c(0,40),
exp = FALSE,
colgap = unit(4,"mm"),
xlog = FALSE,
txt_gp = fpTxtGp(cex = 0.5),
col = fpColors(box = "royalblue",
line = "darkblue",
summary = "royalblue"))`
Here's the data (output from dput):
structure(list(number_of_patients = c(36L, 20L, 56L, 51L, 39L,
125L, 5L, 528L, 32L, 127L, 177L, 129L), overall_survival_mean_of_months = c(7.3,
10.8, 10, 10.8, 5, 14.5, 9.5, 2.9, 14.6, 6.7, 9.3, 4), fulltitle = c("A 2012", "B 2017", "B 1993", "H 2013", "K 2012",
"L 2017", "M 2001", "N 2000", "S 2018",
"S 2013", "S 2005", "S 1992"), CILower = c(5.32596600574852,
8.15155547937496, 8.41725166935702, 9.14147970759323, 3.10340948571217,
13.44062219175, 4.20311095874991, 2.38454718425576, 12.506220764558,
5.64899685123535, 8.40973511344699, 2.95717598838621), CIUpper = c(9.27403399425148,
13.448444520625, 11.582748330643, 12.4585202924068, 6.89659051428783,
15.55937780825, 14.7968890412501, 3.41545281574424, 16.693779235442,
7.75100314876465, 10.190264886553, 5.04282401161379), refnum = c(1,
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)), class = "data.frame", row.names = c(NA,
-12L))
