Add mutate.R and setLabels.R

DESCRIPTION

@@ -35,7 +35,8 @@ Collate:
     'unittest.R'
     'between.R'
     'filter.R'
-    'hy_update_labels.R'
+    'setLabels.R'
+    'mutate.R'
     'rename.R'
     'select.R'
     'slice.R'

NAMESPACE

@@ -1,16 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(filter,hyperSpec)
+S3method(mutate,hyperSpec)
 S3method(rename,hyperSpec)
 S3method(select,hyperSpec)
 S3method(slice,hyperSpec)
 S3method(transmute,hyperSpec)
 export(between)
 export(hySpc.dplyr.unittest)
-export(hy_update_labels)
+export(setLabels)
+export(setLabels_rename)
+export(setLabels_select)
+export(setLabels_transmute)
 exportMethods(between)
 import(magrittr)
 importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
@@ -20,6 +25,7 @@ importFrom(hyperSpec,.fix_spc_colnames)
 importFrom(hyperSpec,chk.hy)
 importFrom(hyperSpec,labels)
 importFrom(methods,setMethod)
+importFrom(rlang,enquos)
 importFrom(rlang,quo_get_expr)
 importFrom(rlang,quo_name)
 importFrom(testthat,ListReporter)

R/mutate.R

@@ -0,0 +1,60 @@
+#' mutate for hyperSpec object
+#'
+#' `mutate` adds new variables and preserves all the existing variables.
+#' Special column `$spc` contains the spectra matrix.
+#'
+#' @inheritParams dplyr::mutate
+#'
+#' @return hyperSpec object.
+#' @include unittest.R
+#' @include setLabels.R
+#' @seealso [dplyr::mutate()]
+#' @importFrom hyperSpec chk.hy
+#' @importFrom hyperSpec labels labels<-
+#' @importFrom rlang enquos
+#' @importFrom rlang quo_name
+#' @importFrom rlang quo_get_expr
+#' @importFrom dplyr mutate
+#' @export
+#'
+#' @examples
+#' laser %>%
+#'   mutate (t, filename)
+#'   head # => results in a hyperSpec object
+#' laser %>%
+#'    mutate (-spc) # => results in a hyperSpec object
+#' laser %>%
+#'    mutate (spc2 = spc*2) %>%
+#'    mutate (spc2) %>%
+#'    mutate (spc2*2) # => results in a hyperSpec object
+mutate.hyperSpec <- function(.data, ...) {
+
+    # Check if user passed in a hyperSpec object
+    chk.hy(.data)
+
+    # Pass mutate arguments to dplyr::mutate
+    res <- mutate(.data@data, ...)
+    .data@data <- res
+    .data
+}
+
+.test(mutate.hyperSpec) <- function() {
+  context("mutate.hyperSpec")
+
+  test_that("non hyperSpec objects are rejected", {
+    df <- data.frame(a = NA, b = NA)
+    expect_error(mutate.hyperSpec(df))
+  })
+
+  test_that("arguments are correctly passed onto mutate/transmute", {
+    hy_tmp <- .testdata
+    hy_tmp@data <- dplyr::mutate(hy_tmp@data, spc*2, spc*3, spc*0)
+    expect_equivalent(mutate.hyperSpec(.testdata, spc*2, spc*3, spc*0), hy_tmp)
+  })
+
+  test_that("$spc can be used for mutation", {
+    hy_tmp <- .testdata
+    hy_tmp@data$spc2 <- hy_tmp@data$spc*2
+    expect_identical(mutate.hyperSpec(.testdata, spc2 = spc*2), hy_tmp)
+  })
+}

R/rename.R

@@ -10,6 +10,7 @@
 #'
 #'
 #' @inheritParams dplyr::rename
+#' @include setLabels.R
 #' @seealso [dplyr::rename()]
 #' @return hyperSpec object. If `$spc` is renamed, the result is an error.
 #' @include unittest.R
@@ -20,48 +21,42 @@
 #'
 #' @examples
 #'
-#' chondro %>%
-#'   rename (region = clusters) %>%
+#' laser %>%
+#'   rename (filename2 = filename) %>%
 #'   head # results in a hyperSpec object
-rename.hyperSpec <- function(.data, ...){
+rename.hyperSpec <- function(.data, ...) {
+
   # Check if user passed in a hyperSpec object
   chk.hy(.data)
+
   # Use dplyr::rename() to rename hyperSpec object data slot
   res <- rename(.data@data, ...)
+
   # Check if $spc was renamed
-  if(!'spc' %in% colnames(res)){
+  if (!'spc' %in% colnames(res)) {
+
     # Throw an error
     stop("$spc cannot be renamed")
-  }else{
-    # Get new and current column names
-    labels.to.update <- setdiff(colnames(res), colnames(.data))
-    labels.to.remove <- setdiff(colnames(.data), colnames(res))
-    # Update the data slot with newly renamed data frame
-    .data@data <- res
-    # Update labels of hyperSpec object
-    new.labels <- lapply(labels(.data, labels.to.update), as.expression)
-    labels(.data)[c(labels.to.remove)] <- NULL
-    labels(.data)[c(labels.to.update)] <- new.labels
-    .data
+  } else {
+
+    # Set labels
+    setLabels_rename(.data, res)
   }
 }
 
 # Begin unit testing (UT)
 .test(rename.hyperSpec) <- function(){
   context("rename.hyperSpec")
 
-  # UT1
   test_that("non hyperSpec objects are rejected", {
     df <- data.frame(a = NA, b = NA)
     expect_error(rename.hyperSpec(df))
   })
 
-  # UT2
   test_that("renaming $spc throws an error", {
     expect_error(rename.hyperSpec(chondro, spc_newname = spc))
   })
 
-  # UT3
   test_that("labels attribute when returning hyperSpec object", {
     tmp <- rename.hyperSpec(chondro, region = clusters)
     tmp <- rename.hyperSpec(tmp, clusters = region)

R/select.R

@@ -13,7 +13,6 @@
 #' @seealso [dplyr::select()]
 #' @return hyperSpec object or data.frame with the selected columns. If the `$spc` is not included in the selection, the result will be a data.frame.
 #' @include unittest.R
-#' @include hy_update_labels.R
 #' @importFrom dplyr select
 #' @importFrom hyperSpec labels labels<-
 #' @export
@@ -34,7 +33,7 @@
 select.hyperSpec <- function(.data, ...) {
   res <- select(.data@data, ...)
   # Update labels
-  hy_update_labels(.data, res)
+  setLabels_select(.data, res)
 }
 
 .test(select.hyperSpec) <- function() {

R/setLabels.R

@@ -0,0 +1,102 @@
+#' Ensure that hyperSpec and non hyperSpec objects have the correct labels
+
+#' @param .data hyperSpec object
+#' @param ... resulting data frame
+#' @return Object with the correct labels
+#' @md
+#'
+#' @importFrom hyperSpec chk.hy
+#' @importFrom hyperSpec labels labels<-
+#' @importFrom rlang enquos
+#' @importFrom rlang quo_name
+#' @importFrom rlang quo_get_expr
+#'
+#' @examples
+#' flu %>%
+#'  setLabels(.wavelength = "f / THz", c = "c / ml")
+#'
+#' @export
+setLabels <- function(.data, ...) {
+
+    # Check if user passed in a hyperSpec object
+    chk.hy(.data)
+    args <- enquos(...)
+    args_names <- names(args)
+    labels2update <- args_names[args_names %in% names(labels(.data))]
+    if (length(args) == 0L) {
+      return(NULL)
+    }
+    for (i in seq_along(args)) {
+        setlabels2 <- quo_name(quo_get_expr(args[[i]]))
+        if (grepl('expr', setlabels2)) {
+            setlabels2 <- as.expression(setlabels2)
+        }
+        labels(.data, labels2update[i]) <- setlabels2
+    }
+    .data
+}
+
+#' @rdname setLabels
+#' @aliases setLabels
+#' @param .data hyperSpec object
+#' @param ... list of columns to update on
+#' @export
+setLabels_transmute <- function(.data, ...) {
+    setLabels(.data, ...)
+}
+
+#' @rdname setLabels
+#' @aliases setLabels
+#' @param .data hyperSpec object
+#' @param res resulting data frame
+#' @export
+setLabels_select <- function(.data, res) {
+
+  # Update labels
+  labels <- labels(.data)[c(".wavelength", colnames(res))]
+  if (is.null(res$spc)) {
+
+    # use attribute to have correct labels when piping into `as.hyperSpec`
+    attr(res, "labels") <- labels
+    res
+  } else {
+    .data@data <- res
+    labels(.data) <- labels
+    .data
+  }
+}
+
+#' @rdname setLabels
+#' @aliases setLabels
+#' @param .data hyperSpec object
+#' @param res resulting data frame
+#' @export
+setLabels_rename <- function(.data, res) {
+    labels.to.update <- setdiff(colnames(res), colnames(.data))
+    labels.to.remove <- setdiff(colnames(.data), colnames(res))
+
+    # Update the data slot with newly renamed data frame
+    .data@data <- res
+
+    # Update labels of hyperSpec object
+    new.labels <- lapply(labels(.data, labels.to.update), as.expression)
+    labels(.data)[c(labels.to.remove)] <- NULL
+    labels(.data)[c(labels.to.update)] <- new.labels
+    .data
+}
+
+.test(setLabels) <- function() {
+  context("setLabels")
+
+  test_that("non hyperSpec objects are rejected", {
+    df <- data.frame(a = NA, b = NA)
+    expect_error(setLabels(df))
+  })
+
+  test_that("labels are correctly set" , {
+      tmp <- laser
+      labels(tmp, ".wavelength") <- "f / THz"
+      expect_equivalent(setLabels(laser, .wavelength = "f /THz"), tmp)
+
+  })
+}