R/log-scale.R

In ShouyeLiu/metaboliteUtility:

#'  log and scale data
#'
#'
#' @param data  A data frame
#' @param var_begin A x-axis variable,character type
#' @param base A y-axis variable,character type
#' @param nan_value  the size of response,character type
#'
#'
#' @name log_scale
#' @rdname log_scale
#' @export
#'
#'

log_scale <- function(data,
                      var_begin=1,
                      var_end = dim(data)[2],
                      base=2,
                      nan_value = 0
)
{
    is.nan.data.frame <- function(x) do.call(cbind, lapply(x, is.nan))
    for (i in var_begin:var_end){
        data[, i]<-as.numeric(as.character(data[, i]));
    }
    data[, var_begin:var_end]<-log((data[, var_begin:var_end]),base = base);
    data[is.nan(data)] <- nan_value;
    data[, var_begin:var_end]<-scale(data[, var_begin:var_end]);
    # please not, the following code applies to whole data
    data[is.nan(data)] <- nan_value;
    return (data)
}