Here is a working example of what I want to do.
# interactive use
subset(iris,Species=="setosa")
# as a function
fn <- function(level,choice) {
x <- paste0(level,"==","'",choice,"'")
subset(iris,eval(parse(text=x)))
}
fn("Species","setosa")
As seen in the function above, I want to specify "Species" and "setosa" programmatically and combine that to form an expression. And that works.
But, that doesn't seem to work for another package that I am working with.
#Biocmanager::install("phyloseq")
library(phyloseq)
data(GlobalPatterns)
# interactive use, this works
subset_taxa(GlobalPatterns,Kingdom=='Archaea')
# as a function, this doesn't work
fn <- function(level,choice) {
x <- paste0(level,"==","'",choice,"'")
subset_taxa(GlobalPatterns,eval(parse(text=x)))
}
fn(level="Kingdom",choice="Archaea")
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'expr' in selecting a method for function 'eval': object 'x' not found
Does the function behave differently or am I doing something wrong?
R 4.0.2
phyloseq_1.34.0
A solution offered by the authors of the phyloseq package:
library(phyloseq)
data(GlobalPatterns)
fn <- function(ps, level, choice) {
x <- paste0(level,"==","'",choice,"'")
oldTax <- data.frame(tax_table(ps))
newTax <- subset(oldTax, eval(parse(text=x)))
tax_table(ps) <- tax_table(as.matrix(newTax))
return(ps)
}
fn(GlobalPatterns, level="Kingdom",choice="Archaea")