add reference samples to divergence outputs

R/getBaselineDivergence.R

@@ -54,11 +54,9 @@
 #' \code{colData} that identifies the baseline samples to be used.
 #' (Default: \code{NULL})
 #' 
-#' @param name \code{Character scalar}. Specifies a column name for storing
-#' divergence results. (Default: \code{"divergence"})
-#' 
-#' @param name.time \code{Character scalar}. Specifies a column name for storing
-#' time differences. (Default: \code{"time_diff"})
+#' @param name \code{Character vector}. Specifies a column name for storing
+#' divergence results. 
+#' (Default: \code{c("divergence", "time_diff", "ref_samples")})
 #' 
 #' @param ... Optional arguments passed into
 #' \code{\link[mia:addDivergence]{mia::addDivergence()}}.
@@ -86,8 +84,8 @@
 #'     reference = "reference",
 #'     group = "subject",
 #'     time.col = "time",
-#'     name = "divergence_from_baseline",
-#'     name.time = "time_from_baseline",
+#'     name = c("divergence_from_baseline", 
+#'         "time_from_baseline", "reference_samples"),
 #'     assay.type = "relabundance",
 #'     method = "bray")
 #' 
@@ -153,20 +151,21 @@ setMethod("getBaselineDivergence", signature = c(x = "SummarizedExperiment"),
         reference <- args[["reference"]]
         time_res <- .get_time_difference(x, time.col, reference)
         # Create a DF to return
-        res <- .convert_divergence_to_df(x, res, time_res, ...)
+        res <- .convert_divergence_to_df(x, res, time_res, reference, ...)
         return(res)
     }
 )
 
 #' @rdname addBaselineDivergence
 #' @export
 setMethod("addBaselineDivergence", signature = c(x = "SummarizedExperiment"),
-    function(x, name = "divergence", name.time = "time_diff", ...){
+    function(
+        x, name = c("divergence", "time_diff", "ref_samples"), ...){
         # Calculate divergence
         res <- getBaselineDivergence(x, ...)
         # Add to colData
         res <- as.list(res) |> unname()
-        x <- .add_values_to_colData(x, res, list(name, name.time), ...)
+        x <- .add_values_to_colData(x, res, name, ...)
         return(x)
     }
 )
@@ -317,7 +316,7 @@ setMethod("addBaselineDivergence", signature = c(x = "SummarizedExperiment"),
     return(res)
 }
 
-# This function get time difference between a sample and its referene sample
+# This function get time difference between a sample and its reference sample
 .get_time_difference <- function(x, time.col, reference){
     # Get timepoints
     time_point <- x[[time.col]]
@@ -330,13 +329,12 @@ setMethod("addBaselineDivergence", signature = c(x = "SummarizedExperiment"),
 
 # This function converts time divergence results to DF object
 .convert_divergence_to_df <- function(
-        x, res, time_res, name = "divergence", name.time = "time_diff", ...){
-    #
-    temp <- .check_input(name, list("character scalar"))
-    #
-    temp <- .check_input(name.time, list("character scalar"))
+        x, res, time_res, reference,
+        name = c("divergence", "time_diff", "ref_samples"), ...){
+    # Validate 'name' param
+    temp <- .check_input(name, list("character vector"), length = 3)
     #
-    df <- DataFrame(res, time_res, row.names = colnames(x))
-    colnames(df) <- c(name, name.time)
+    df <- DataFrame(res, time_res, x[[reference]], row.names = colnames(x))
+    colnames(df) <- name
     return(df)
 }

R/getStepwiseDivergence.R

@@ -102,20 +102,21 @@ setMethod("getStepwiseDivergence", signature = c(x = "ANY"),
         reference <- args[["reference"]]
         time_res <- .get_time_difference(x, time.col, reference)
         # Create a DF to return
-        res <- .convert_divergence_to_df(x, res, time_res, ...)
+        res <- .convert_divergence_to_df(x, res, time_res, reference, ...)
         return(res)
     }
 )
 
 #' @rdname addStepwiseDivergence
 #' @export
 setMethod("addStepwiseDivergence", signature = c(x = "SummarizedExperiment"),
-    function(x, name = "divergence", name.time = "time_diff", ...){
+    function(
+        x, name = c("divergence", "time_diff", "ref_samples"), ...){
         # Calculate divergence
         res <- getStepwiseDivergence(x,  ...)
         # Add to colData
         res <- as.list(res) |> unname()
-        x <- .add_values_to_colData(x, res, list(name, name.time), ...)
+        x <- .add_values_to_colData(x, res, name, ...)
         return(x)
     }
 )

R/utils.R

@@ -6,7 +6,7 @@
 # Borrowed from HoloFoodR.
 .check_input <- function(
         variable, supported_class, supported_values = NULL, limits = NULL,
-        variable_name = .get_name_in_parent(variable)){
+        length = NULL, variable_name = .get_name_in_parent(variable)){
     # Convert supported classes to character
     classes_char <- lapply(supported_class, function(class){
         if( is.null(class) ){
@@ -54,6 +54,11 @@
         msg <- paste0(msg, ")")
     }
 
+    # If length was provided
+    if( !is.null(length) ){
+        msg <- paste0(msg, " The length must be ", length, ".")
+    }
+
     # List all the input types. Run the check if the variable must be that type.
     # If correct type was found, change the result to TRUE.
     input_correct <- FALSE
@@ -128,6 +133,10 @@
             input_correct <- FALSE
         }
     }
+    # Check length if provided
+    if( !is.null(length) && length(variable) != length ){
+        input_correct <- FALSE
+    }
     # Give error if variable was not correct type
     if( !input_correct ){
         stop(msg, call. = FALSE)