#' Get a quantititative variable from microbe directory
#'
#' This function returns a dataframe of one of the quantitative
#' variable from the microbe directory for each of the test_set
#' and background set
#'
#' @param database test_set background_set
#' @export
#' @examples
#' get_quantitative_variable(microbe_directory=microbe_directory, test_set=test_set, background_set=background_set, variable="optimal_ph")
get_quantitative_variable <- function(microbe_directory=microbe_directory,
test_set=test_set,
background_set=background_set,
variable="optimal_ph"){
if (!(variable %in% c("optimal_ph", "optimal_temperature"))){
stop(paste0("There is no quantitative variable '", variable, "' in The Microbe Directory"))
}
test_set_ids <- intersect(rownames(microbe_directory), test_set)
test_set_variable <- data.frame(microbe_directory[test_set_ids, variable])
test_set_variable$type <- "test_set"
colnames(test_set_variable) <- c(variable, "type")
background_set_ids <- intersect(rownames(microbe_directory), background_set)
background_set_variable <- data.frame(microbe_directory[background_set_ids, variable])
background_set_variable$type <- "background_set"
colnames(background_set_variable) <- c(variable, "type")
dat <- data.frame(rbind(test_set_variable, background_set_variable))
rownames(dat) <- append(test_set_ids, background_set_ids)
cat("Removing rows with no data...\n")
dat <- na.omit(dat)
return(dat)
}
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