InterpretMSSpectrum (version 1.5.2)

fml2expr: Turn text with chemical formulas into expression vector.

Description

It is often helpful to annotate a Figure with chemical formulas. However, to increase readability of chemical formulas, certain conventions have to be met. These concern, among others, superscript and subscript text which, in R, can only be provided via expressions. `fml2expr` will convert any character vector into an expression vector, aiming to identify and format potential contained chemical formulas.

Usage

fml2expr(x, expr = TRUE)

Value

A vector of expressions.

Arguments

x

Character vector containing chemical formulas.

expr

Will return vector of characters when FALSE and expressions when TRUE.

Examples

texts <- c(
  "C6H12Cl6",         # simple formula
  "H3Na",             # simple formula
  "Text with blank",  # simple text
  "A1B2",             # No valid elements but looks like formula
  "Fe(NO3)3",         # group with index
  "SO4^2-",           # charged molecule
  "Na+", "Cl-",       # simple ions
  paste0("H", intToUtf8(0x2082), "O"), # unicode-subscript
  "Ca(OH)2-"          # group with index and charge
)

# Check that all examples can be converted to expression
all(sapply(texts , function(x) { !inherits(try(fml2expr(x), silent=TRUE), "try-error") }))
exprs <- fml2expr(texts)
str(exprs)

# Plot with legend
plot(1:10, 1:10, pch = 16, col = 1:10, xlim = c(0, 11), ylim = c(0, 11))
legend("topright", legend = exprs, col = 1:10, pch = 16, title = "Formeln")

# Careful! text() does not accept an expression vector
text(3:4,3:4,labels=exprs[3:4])
for (i in 5:6) text(i,i,labels=exprs[[i]])

# you can also return a named character vector (names are input, values are modified)
fml2expr(texts, expr = FALSE)