R/scRepertoire_v2_functions.R

In APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

# A variety of scRepertoire v2 functions copied during beta testing,
# all permissions granted by the owner + both authors

.theCall <- function(df, x, check.df = TRUE) {
    x <- .convertClonecall(x)
    if(check.df) {
      if(inherits(df, "list") & !any(colnames(df[[1]]) %in% x)) {
        stop(
            "Check the clonal variabe (cloneCall) being used in the function, it does not appear in the data provided.",
            call. = FALSE
        )
      } else if (inherits(df, "data.frame") & !any(colnames(df) %in% x)) {
        stop(
            "Check the clonal variabe (cloneCall) being used in the function, it does not appear in the data provided.",
            call. = FALSE
        )
      }
    }
    return(x)
}

.convertClonecall <- function(x) {

    clonecall_dictionary <- hash::hash(
        "gene" = "CTgene",
        "genes" = "CTgene",
        "ctgene" = "CTgene",
        "nt" = "CTnt",
        "nucleotide" = "CTnt",
        "nucleotides" = "CTnt",
        "ctnt" = "CTnt",
        "aa" = "CTaa",
        "amino" = "CTaa",
        "ctaa" = "CTaa",
        "gene+nt" = "CTstrict",
        "strict" = "CTstrict",
        "ctstrict" = "CTstrict"
    )

    possible_clonecall <- clonecall_dictionary[[tolower(strip_unquoted_spaces(x))]]
    if (!is.null(possible_clonecall)) return(possible_clonecall)
    x
}