Better tests and interactive plots (#140)

* better tests * better plotting, split and rel * add a couple other errors to `check_OpenSpecy()` * add contributors * submit v1.0.3 --------- Co-authored-by: Zacharias Steinmetz <[email protected]>
wincowgerDEV · Sep 13, 2023 · 8a3197b · 8a3197b
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.2
-Date: 2023-09-05 13:16:55 UTC
-SHA: 92ce663a7883e3c9886fb7c2ada24fd7deb4c49b
+Version: 1.0.3
+Date: 2023-09-13 15:19:30 UTC
+SHA: 2ff9c1a9be7e2e3c99747f8f65302223b7951830
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: OpenSpecy
 Type: Package
 Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
-Version: 1.0.2
-Date: 2023-09-05
+Version: 1.0.3
+Date: 2023-09-13
 Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       email = "[email protected]",
       comment = c(ORCID = "0000-0001-9226-3104")),
@@ -38,6 +38,9 @@ Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
     person("Laura A. T.", "Markley", role = c("ctb"),
       comment = c(ORCID = "0000-0003-0620-8366")),
     person("Shreyas", "Patankar", role = c("ctb", "dtc")),
+    person("Rachel", "Kozloski", role = c("ctb", "dtc"),
+      comment = c(ORCID = "0000-0003-1211-9351")),
+    person("Samiksha", "Singh", role = c("ctb")),
     person("Katherine", "Lasdin", role = c("ctb")),
     person("National Renewable Energy Laboratory", role = c("fnd")), 
     person("Possibility Lab", role = c("fnd")))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# OpenSpecy 1.0.3
+
+## Minor Improvements
+
+- Simplify `check_OpenSpecy()`
+- Improve unit tests
+- Improve interactive plots
+
+
 # OpenSpecy 1.0.2
 
 ## Bug Fixes

diff --git a/R/as_OpenSpecy.R b/R/as_OpenSpecy.R
@@ -71,8 +71,8 @@
 #' Focal Plane Array, CCD\cr
 #' \code{instrument_mode}: \tab Instrument modes/settings, e.g.
 #' transmission, reflectance \cr
-#' \code{intensity_units*}: \tab Units of the intensity values for the spectrum, options
-#' transmittance, reflectance, absorbance \cr
+#' \code{intensity_units*}: \tab Units of the intensity values for the spectrum,
+#' options transmittance, reflectance, absorbance \cr
 #' \code{spectral_resolution}: \tab Spectral resolution, e.g. 4/cm \cr
 #' \code{laser_light_used}: \tab Wavelength of the laser/light used, e.g.
 #' 785 nm \cr
@@ -108,10 +108,10 @@
 #' data("raman_hdpe")
 #'
 #' # Inspect the spectra
-#' raman_hdpe # See how OpenSpecy objects print.
-#' raman_hdpe$wavenumber # Look at just the wavenumbers of the spectra.
-#' raman_hdpe$spectra # Look at just the spectral intensities data.table.
-#' raman_hdpe$metadata # Look at just the metadata of the spectra.
+#' raman_hdpe # see how OpenSpecy objects print.
+#' raman_hdpe$wavenumber # look at just the wavenumbers of the spectra.
+#' raman_hdpe$spectra # look at just the spectral intensities data.table.
+#' raman_hdpe$metadata # look at just the metadata of the spectra.
 #'
 #' # Creating a list and transforming to OpenSpecy
 #' as_OpenSpecy(list(wavenumber = raman_hdpe$wavenumber,
@@ -127,8 +127,8 @@
 #'                             spectra = raman_hdpe$spectra$intensity))
 #'
 #' # Test that the spectrum is formatted as an OpenSpecy object.
-#' is_OpenSpecy(raman_hdpe)  #should be TRUE
-#' is_OpenSpecy(raman_hdpe$spectra) #should be FALSE
+#' is_OpenSpecy(raman_hdpe)
+#' is_OpenSpecy(raman_hdpe$spectra)
 #'
 #' @author
 #' Zacharias Steinmetz, Win Cowger
@@ -314,33 +314,39 @@ is_OpenSpecy <- function(x) {
 #' @importFrom data.table is.data.table
 #' @export
 check_OpenSpecy <- function(x) {
-  if(!(is_OpenSpecy(x)))
-    stop("object 'x' is not of class 'OpenSpecy'", call. = F)
-  if(!identical(names(x), c("wavenumber", "spectra", "metadata")))
-    stop("names of the object components are incorrect", call. = F)
+  if(!(cos <- is_OpenSpecy(x)))
+    warning("Object 'x' is not of class 'OpenSpecy'", call. = F)
+  if(!(cln <- identical(names(x), c("wavenumber", "spectra", "metadata"))))
+    warning("Names of the object components are incorrect", call. = F)
   if(!(cw <- is.vector(x$wavenumber)))
     warning("Wavenumber is not a vector", call. = F)
+  if(!(cwn <- !any(is.na(x$wavenumber))))
+    warning("Wavenumber values have NA", call. = F)
   if(!(cs <- is.data.table(x$spectra)))
-    message("Spectra are not of class 'data.table'")
+    warning("Spectra are not of class 'data.table'", call. = F)
+  if(!(csn <- !any(vapply(x$spectra, function(x){all(is.na(x))},
+                          FUN.VALUE = logical(1)))))
+    warning("Some of the spectra have all NA values", call. = F)
   if(!(cm <- is.data.table(x$metadata)))
-    message("Metadata are not a 'data.table'")
+    warning("Metadata are not a 'data.table'", call. = F)
   if(!(cr <- ncol(x$spectra) == nrow(x$metadata)))
     warning("Number of columns in spectra is not equal to number of rows ",
             "in metadata", call. = F)
+  if(!(csz <- nrow(x$spectra) != 0))
+    warning("There are no spectral intensities in your spectra", call. = F)
   if(!(cl <- length(x$wavenumber) == nrow(x$spectra)))
     warning("Length of wavenumber is not equal to number of rows in spectra",
             call. = F)
   if(!(cu <- length(unique(names(x$spectra))) == ncol(x$spectra)))
     warning("Column names in spectra are not unique", call. = F)
   if(!(cv <- length(unique(names(x$metadata))) == ncol(x$metadata)))
-    message("Column names in metadata are not unique")
+    warning("Column names in metadata are not unique", call. = F)
   if(!(co <- identical(order(x$wavenumber), 1:length(x$wavenumber)) |
        identical(order(x$wavenumber), length(x$wavenumber):1)))
-    message("This is technically an 'OpenSpecy' object but wavenumbers ",
-            "should be a continuous sequence for all OpenSpecy functions to ",
-            "run smoothly")
+    warning("Wavenumbers should be a continuous sequence for all OpenSpecy ",
+            "functions to run smoothly", call. = F)
 
-  chk <- all(cw, cs, cm, cr, cl, cu, cv, co)
+  chk <- all(cw, cs, cm, cr, cl, cu, cv, co, csz, csn, cwn, cln, cos)
 
   return(chk)
 }

diff --git a/R/io_spec.R b/R/io_spec.R
@@ -144,6 +144,6 @@ read_spec <- function(file, share = NULL, method = NULL, ...) {
 #'
 #' @export
 as_hyperSpec <- function(x) {
-    new("hyperSpec", spc = as.matrix(transpose(x$spectra)),
-        wavelength = x$wavenumber)
+  new("hyperSpec", spc = as.matrix(transpose(x$spectra)),
+      wavelength = x$wavenumber)
 }
diff --git a/README.md b/README.md
@@ -55,10 +55,11 @@ library(OpenSpecy)
 run_app()
 ```
 
-## See [package vignette](http://wincowger.com/OpenSpecy-package/articles/sop.html) for a detailed standard operating procedure.
-
 ## Simple workflow for single spectral identification
 
+See [package vignette](http://wincowger.com/OpenSpecy-package/articles/sop.html)
+for a detailed standard operating procedure.
+
 ```r
 # Fetch current spectral library from https://osf.io/x7dpz/
 get_lib("derivative")
@@ -85,11 +86,11 @@ top_matches <- match_spec(raman_proc, library = spec_lib, na.rm = T, top_n = 5,
                           add_library_metadata = "sample_name",
                           add_object_metadata = "col_id")
 
-#Print the top 5 results with relevant metadata
+# Print the top 5 results with relevant metadata
 top_matches[, c("object_id", "library_id", "match_val", "SpectrumType",
                 "SpectrumIdentity")]
 
-#Get all metadata for the matches
+# Get all metadata for the matches
 get_metadata(spec_lib, logic = top_matches$library_id)
 ```
 
@@ -101,6 +102,6 @@ Needs an Open Source Community: Open Specy to the Rescue!”
 *Analytical Chemistry*, **93**(21), 7543–7548. doi:
 [10.1021/acs.analchem.1c00123](https://doi.org/10.1021/acs.analchem.1c00123).
 
-Cowger W, Steinmetz Z (2023). “OpenSpecy: Analyze, Process,
-Identify, and Share Raman and (FT)IR Spectra.” *R package*, **1.0.2**.
+Cowger W, Steinmetz Z, Leong N, Faltynkova A (2023). “OpenSpecy: Analyze,
+Process, Identify, and Share Raman and (FT)IR Spectra.” *R package*, **1.0.3**.
 [https://github.com/wincowgerDEV/OpenSpecy-package](https://github.com/wincowgerDEV/OpenSpecy-package).
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,8 +1,6 @@
 url: http://wincowger.com/OpenSpecy-package/
 template:
   bootstrap: 5
-development:
-  mode: auto
 articles:
 - title: Articles
   navbar: ~

diff --git a/cran-comments.md b/cran-comments.md
@@ -10,14 +10,9 @@
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
+0 errors | 0 warnings | 0 notes
 
 
 ## Comments
 
-    Possibly misspelled words in DESCRIPTION:
-      wavenumber (50:62)
-
-The word is spelled correctly, see https://en.wikipedia.org/wiki/Wavenumber
-
 For further details, see NEWS.md
diff --git a/man/OpenSpecy-package.Rd b/man/OpenSpecy-package.Rd
diff --git a/man/as_OpenSpecy.Rd b/man/as_OpenSpecy.Rd
diff --git a/tests/testthat/test-as_OpenSpecy.R b/tests/testthat/test-as_OpenSpecy.R
@@ -62,21 +62,21 @@ test_that("as_OpenSpecy() generates OpenSpecy objects", {
 test_that("check_OpenSpecy() work as expected", {
   os <- as_OpenSpecy(df)
   check_OpenSpecy(os) |> expect_true()
-  check_OpenSpecy(df) |> expect_error()
+  check_OpenSpecy(df) |> expect_error() |> expect_warning() |> expect_warning() |> expect_warning() |> expect_warning()
 
   osv <- osn <- oss <- ost <- osl <- os
 
   osv$wavenumber <- list(osv$wavenumber)
   check_OpenSpecy(osv) |> expect_false() |> expect_warning()
 
   names(osn) <- 1:3
-  check_OpenSpecy(osn) |> expect_error()
+  check_OpenSpecy(osn) |> expect_error() |> expect_warning() |> expect_warning()|> expect_warning() |> expect_warning()
 
   oss$wavenumber <- sample(oss$wavenumber)
-  check_OpenSpecy(oss) |> expect_false() |> expect_message()
+  check_OpenSpecy(oss) |> expect_false() |> expect_warning()
 
   class(ost$metadata) <- class(ost$spectra) <- "data.frame"
-  check_OpenSpecy(ost) |> expect_false() |> expect_message() |> expect_message()
+  check_OpenSpecy(ost) |> expect_false() |> expect_warning() |> expect_warning()
 
   osl$metadata <- rbind(osl$metadata, osl$metadata)
   osl$spectra <- osl$spectra[-1]
@@ -110,3 +110,4 @@ test_that("'OpenSpecy' objects are transcribed to and from 'hyperSpec' objects",
   expect_equal(openhyper$wavenumber, hyper@wavelength)
   expect_equal(unlist(openhyper$spectra$V1),unname(t(hyper$spc)[,1]))
 })
+
diff --git a/tests/testthat/test-interactive_plots.R b/tests/testthat/test-interactive_plots.R
@@ -6,11 +6,16 @@ test_that("plotly_spec() handles input errors correctly", {
 })
 
 test_that("plotly_spec() generates 'plotly' object", {
-  plotly_spec(raman_hdpe) |>
+  plotly_spec(x = raman_hdpe, x2 = raman_hdpe) |>
     expect_silent() |>
     expect_s3_class("plotly")
 })
 
+test_that("interactive_plot() generates 'plotly' object with single or multiple spectra from map", {
+  interactive_plot(map, x2 = raman_hdpe, select = 2:3) |>
+        expect_s3_class("plotly")
+})
+
 test_that("heatmap_spec() handles input errors correctly", {
   heatmap_spec(1:1000) |> expect_error()
 })
@@ -21,13 +26,7 @@ test_that("heatmap_spec() generates 'plotly' object", {
     expect_s3_class("plotly")
 })
 
-test_that("heatmap_spec() can handle all NA", {
-  heatmap_spec(map, z = map$metadata$y, sn = map$metadata$y, min_sn = 100) |>
-    expect_silent()
-})
-
 test_that("interactive_plot() generates 'plotly' object", {
-  interactive_plot(map, x2 = raman_hdpe, select = 2:3) |>
-    expect_silent() |>
-    expect_s3_class("plotly")
+  interactive_plot(map, x2 = raman_hdpe, select = 2) |>
+        expect_s3_class("plotly")
 })
diff --git a/tests/testthat/test-match_spec.R b/tests/testthat/test-match_spec.R
@@ -20,7 +20,7 @@ test_that("match_spec() returns correct structure with AI", {
   get_lib("model", path = tmp)
   lib <- load_lib(type = "model", path = tmp)
 
-  expect_error(check_OpenSpecy(lib))
+  check_OpenSpecy(lib) |> expect_error() |> expect_warning() |> expect_warning() |> expect_warning() |> expect_warning() |> expect_warning()
 
   set.seed(47)
   rn <- runif(n = length(unique(lib$variables_in)))
@@ -119,7 +119,7 @@ test_that("filter_spec() handles input errors correctly", {
 test_that("filter_spec() returns erroneous OpenSpecy object when removing all spectra", {
   os_filtered <- filter_spec(test_lib, logic = rep(F, ncol(test_lib$spectra))) |>
     expect_silent()
-  expect_warning(check_OpenSpecy(os_filtered))
+  check_OpenSpecy(os_filtered) |> expect_warning() |> expect_warning()
   expect_equal(ncol(os_filtered$spectra), 0)
   expect_equal(nrow(os_filtered$metadata), 0)
 })

diff --git a/vignettes/.gitignore b/vignettes/.gitignore
@@ -1 +1,2 @@
 *.R
+*.html