matrix R convert from numeric to characters provided in csv

Question

I am new to using R and learning how to create forest plots using the forestplot function.

I am struggling with labeling y-axis of the forest plot using:

labeltext = matrix()

When I use this:

labeltext = matrix(c(data$BCT, data$present), nrows=40, ncol=2, byrow=TRUE, dimnames=NULL)

I get a numeric matrix and R ignores the text in the scv file I provide.

It seems to work when I make a matrix for one column. How do I label y-axis using two columns from a csv file?

I want to achieve something like this:

but instead of 'reference', 'lact', and 'diet' it should say 'BCT' and 'present'.

I want a forest plot that has 'BCT' (column 1) and 'present' (column 2) as the y-axis labels. SMD is the effect measure, and upper_limit and lower_limit are CI. See sample data below

Here is the code:

library(forestplot)
labeltext = matrix(c(data$BCT, data$present), nrow = 40, ncol = 2, byrow = TRUE, dimnames = NULL)
is_summary = FALSE
forestplot(labeltext,
           graph.pos = 2,
           mean = data$SMD,
           lower = data$"lower_limit",
           upper = data$"upper_limit",
           is.summary = is_summary, 
           xlab = "<-------Comparator Better---------------Main Intervention Better-------->",
           line.margin = unit (0.8, "cm"),
           lineheight = unit (0.5, "cm"),
           hrlz.lines =TRUE,
           col = fpColors(box = "darkred", lines = "grey", summary = "black"),
           graphwidth = unit (10, "cm"))


# Sample Input Data
data <- structure(list(
BCT = c("Adding objects to the environment (12.5) ", "Adding objects to the environment (12.5) ", "Action planning (1.4)", "Action planning (1.4)", "Body changes (12.6) ", "Body changes (12.6) ", "Behavioural practice/rehearsal (8.1)", "Behavioural practice/rehearsal (8.1)", "Credible source (9.2)", "Credible source (9.2)", "Demonstration of the behaviour (6.1) ", "Demonstration of the behaviour (6.1) ", "Feedback on behaviour (2.2) ", "Feedback on behaviour (2.2) ", "Goal setting (behaviour) (1.1)", "Goal setting (behaviour) (1.1)", "Graded tasks (8.7)", "Graded tasks (8.7)",  "Generalisation of target behaviour (8.6) ", "Generalisation of target behaviour (8.6) ", "Information about health consequences (5.1)", "Information about health consequences (5.1)", "Instruction on how to perform the behaviour (4.1)", "Instruction on how to perform the behaviour (4.1)", "Monitoring of behaviour by others without feedback (2.1)", "Monitoring of behaviour by others without feedback (2.1)",  "Monitoring of outcomes of behaviour without feedback (2.5)", 
"Monitoring of outcomes of behaviour without feedback (2.5)", "Problem solving (1.2) ", "Problem solving (1.2) ", "Social Comparison (6.2)", "Social Comparison (6.2)", "Self-monitoring of behaviour (2.3) ", "Self-monitoring of behaviour (2.3) ", "Self-monitoring of outcome(s) of behaviour (2.4) ", "Self-monitoring of outcome(s) of behaviour (2.4) ", "Social support (emotional) (3.3)", "Social support (emotional) (3.3)", "Social support (unspecified) (3.1) ", "Social support (unspecified) (3.1) "), 
present = c("present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present", "present ", "not present"), 
SMD = c(1.69, 0.42, 0.78, 0.4, 0.36, 0.57, 0.71, 0.4, 2.23, 0.31, 0.32, 0.63, 0.45, 0.58, 0.79, 0.26, 0.55, 0.56, 1.39, 0.4, 0.6, 0.46, 0.7, 0.34, 2.53, 0.47, 0.36, 0.62, 0.2, 0.7, 0.03, 0.66, 0.68, 0.47, 1.14, 0.4, 1.13, 0.44, 0.67, 0.52), 
lower_limit = c(-1.49, 0.22, -0.4, 0.06, 0.08, -0.33, -0.34, -0.04, 0.15, 0.2, 0.14, -0.4, -0.25, -0.26, -0.19, 0.11, -0.66, 0.23, -0.68, 0.19, -0.35, 0.11, -0.46, 0.15, 1.36, 0.05, -0.07, -0.2, -0.01, -0.18, -0.42, -0.14, -0.4, 0.06, -0.84, 0.16, -1.47, 0.24, -0.93, 0.27), 
upper_limit = c(4.87, 0.62, 1.95, 0.74, 0.65, 1.48, 1.75, 0.84, 4.32, 0.42, 0.51, 1.67, 1.15, 1.43, 1.77, 0.41, 1.77, 0.89, 3.46, 0.6, 1.55, 0.81, 1.87, 0.53, 3.7, 0.89, 0.78, 1.43, 0.41, 1.58, 0.47, 1.46, 1.77, 0.88, 3.12, 0.64, 3.72, 0.65, 2.28, 0.78)), 
.Names = c("BCT", "present", "SMD", "lower_limit", "upper_limit"), 
row.names = c(NA, -40L), class = "data.frame")

It's easier to help you if you provide a [reproducible example](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) with sample input. Perhaps provide a link that shows the desired output you are after. — MrFlick, May 03 '17 at 15:48
@MrFlick here is the link to my csv file: https://cityaliyaamirova.sharefile.com/d-s389ae8f919044938 . I want to use the first two columns of the file to label y-axis on the forest plot. — Aliya, May 03 '17 at 17:19
@MrFlick Thank you it worked! :) how do I vote for your answer on here? — Aliya, May 03 '17 at 23:30
@MrFlick, I do not have enough 'reputation' to vote your answer up. — Aliya, May 11 '17 at 15:00

score 0 · Accepted Answer · answered May 03 '17 at 23:41

It's likely you imported your character data as factors. When you use simplifing functions like c() and matrix() to reshape factors, they get converted to numeric values since matrices can't contain factors. A more careful transformation would be

labeltext = as.matrix(data.frame(data$BCT, data$present))

matrix R convert from numeric to characters provided in csv

1 Answers1