Expression using greek letters in R

Question

[Bastien Hervé]

Hello,

I'm trying to detect greek letters in a string in R and convert my string to an expression. I know there are multiple threads about this (https://stackoverflow.com/questions/6044800/adding-greek-character-to-axis-title). But I can't find a way to paste multiple greek letters at once...

My data :

str <- "myrangammadomsequenmuce15874withsomephigreek2874lettergamma"

I want to get something like this :

expression(paste("myran", gamma, "domsequen", mu, "ce15874withsome", phi, "greek2874letter", gamma)

I tried to split my string using multiple delimiters but when I want to collapse I don't know which was the delimiter used.

Thanks !

[GenoMax]

@Bastien: Pure R questions like this are best asked elsewhere.

Edit: Perhaps there is a bioinformatics angle. Are you trying to label an axis with a greek character?

[Bastien Hervé]

I'm trying to display labels for IgH locus of mm10 (gamma3, gamma1, mu etc...)

I have GRanges with these locus as name and I want to create an expression vector with it

[zx8754]

Probably would be better if you could share example GRanges object, and expected output.

[Bastien Hervé]

Why do you need the entire GRanges ?

In my GRanges, first line I have as name : myrangammadomsequenmuce15874withsomephigreek2874lettergamma

I want to create an expression with that and append this expression to a vector of expression...etc

Then second line, I take the name, then I append the vector of expression.

I know how to loop over my GRanges and append a vector. I'm just stuck at expression creation

[zx8754]

OK, still wondering how did you end up with that string.

[Bastien Hervé]

I'll ask users to input their own string. As everyone know here, user are unpredictable. I expect this string will be the most wtf string I will got from my users :)

[zx8754]

How did you come up with that string, where is it from?

[Bastien Hervé]

my str string is pure training but covers all cases.

Answer 1

[Bastien Hervé]

After 1 day I've found a really dirty way !

library(stringr)
str <- "myrangammadomsequenmuce15874withsomephigreek2874lettergamma"
str <- gsub("gamma", "'~gamma~'", str)
str <- gsub("phi", "'~phi~'", str)
str <- gsub("mu", "'~mu~'", str)

str
#[1] "myran'~gamma~'domsequen'~mu~'ce15874withsome'~phi~'greek2874letter'~gamma~'"

if (substr(str,1,1) == "'"){
    str <- paste0("expression(",substr(str,3,nchar(str)))
} else{
    str <- paste0("expression('",str)
}
if (str_sub(str,-1,-1) == "'"){
    str <- paste0(substr(str,1,nchar(str)-2),")")
} else{
    str <- paste0(str,"')")
}
result <- eval(parse(text=str))

result
#expression("myran" ~ gamma ~ "domsequen" ~ mu ~ "ce15874withsome" ~ phi ~ "greek2874letter" ~ gamma)

Answer 2

[zx8754]

I don't have the full answer, but below should get you started:

library(stringr)

x <- "myrangammadomsequenmuce15874withsomephigreek2874lettergamma"
greek <- "gamma|mu|phi"

str_split(x, greek)
# [[1]]
# [1] "myran"           "domsequen"       "ce15874withsome" "greek2874letter" ""  
str_extract_all(x, greek)
# [[1]]
# [1] "gamma" "mu"    "phi"   "gamma"
str_locate_all(x, greek)
# [[1]]
#      start end
# [1,]     6  10
# [2,]    20  21
# [3,]    37  39
# [4,]    55  59

[Bastien Hervé]

I got something like this for each greek letters but I can't figure it out how to create my expression in once. Because I can't iterate on my paste for each greek letter, then, at the end create the expression. Or greek letters will be display as normal string.

Answer 3

[cpad0112]

can you get greek letters converted to uTF(8) in R (from english words to greek to alphabets)? If so, you can use lookaround in R.

>gamma=intToUtf8(0x03B3)
>mu=intToUtf8(0x03BC)
>phi=intToUtf8(0x03D5)
> test1=paste0("myran", gamma, "domsequen", mu, "ce15874withsome", phi, "greek2874letter", gamma)
> test1
[1] "myranγdomsequenμce15874withsomeϕgreek2874letterγ"
> strsplit(test1,"(?<=\\W)(?=\\w)|(?<=\\w)(?=\\W)|(?<=\\W)(?=\\W)", perl = T)
[[1]]
[1] "myran"           "γ"               "domsequen"       "μ"               "ce15874withsome"
[6] "ϕ"               "greek2874letter" "γ"

[Bastien Hervé]

Nice one, problem is that I don't have test1 as you wrote it :

test1=paste0("myran", gamma, "domsequen", mu, "ce15874withsome", phi, "greek2874letter", gamma)

I just have my string :

test1 <- "myrangammadomsequenmuce15874withsomephigreek2874lettergamma"

I need to detect my greek letters word in my string (maybe as zx8754 suggest above), to transform them into "real" greek letters then after to paste the result