v0.17.3 increase test coverage

jeffkimbrel · Oct 7, 2024 · eee3233 · eee3233
1 parent 9889cda
commit eee3233
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.17.2
+Version: 0.17.3
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7213-9392"))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,5 @@
+# qSIP2 0.17.3
+
 # qSIP2 0.17.2
 
 # qSIP2 0.17.1

diff --git a/R/get_resample_data.R b/R/get_resample_data.R
@@ -15,12 +15,21 @@
 get_resample_data <- function(qsip_data_object,
                               type = "all",
                               pivot = FALSE) {
-  if (!"qsip_data" %in% class(qsip_data_object)) {
-    stop("qsip_data_object should be class <qsip_data>", call. = FALSE)
-  } else if (length(qsip_data_object@resamples) == 0) {
-    stop("this function requires a qsip object that has been run through run_resampling()", call. = FALSE)
+  if (isFALSE(is_qsip_resampled(qsip_data_object, error = FALSE))) {
+    stop("This function requires a qsip object that has been run through run_resampling()", call. = FALSE)
   }
 
+  # error if type is not one of "all", "unlabeled", or "labeled"
+  if (!type %in% c("all", "unlabeled", "labeled")) {
+    stop("type must be one of 'all', 'unlabeled', or 'labeled'", call. = FALSE)
+  }
+
+  # error if pivot is not TRUE/FALSE
+  if (!isTRUE(pivot) && !isFALSE(pivot)) {
+    stop("pivot must be TRUE or FALSE", call. = FALSE)
+  }
+
+
   # bind variables
   feature_id <- resample <- NULL
 
@@ -32,8 +41,6 @@ get_resample_data <- function(qsip_data_object,
     df <- dplyr::bind_rows(qsip_data_object@resamples$u) |> dplyr::select(-type)
   } else if (type == "labeled") {
     df <- dplyr::bind_rows(qsip_data_object@resamples$l) |> dplyr::select(-type)
-  } else {
-    stop("type must be one of 'all', 'unlabeled', or 'labeled'", call. = FALSE)
   }
 
 

diff --git a/R/plot_feature_resamplings.R b/R/plot_feature_resamplings.R
@@ -22,7 +22,7 @@ plot_feature_resamplings <- function(qsip_data_object,
                                      confidence = 0.9,
                                      intervals = "") {
 
-  if (isFALSE(is_qsip_filtered(qsip_data_object, error = FALSE))) {
+  if (isFALSE(is_qsip_resampled(qsip_data_object, error = FALSE))) {
     stop("This function requires a qsip object that has been run through run_resampling()", call. = FALSE)
   }
 

diff --git a/R/plot_sample_curves.R b/R/plot_sample_curves.R
@@ -1,6 +1,6 @@
 #' Plot qSIP sample data density curves
 #'
-#' @param qsip_data (*qsip_data*) qSIP object
+#' @param qsip_data_object (*qsip_data*) qSIP object
 #' @param colors (*character*) A named vector of colors for each isotope (optional)
 #' @param title (*character*) An optional title for the plot
 #'
@@ -10,23 +10,29 @@
 #'
 #' @family "visualizations"
 
-plot_sample_curves <- function(qsip_data,
+plot_sample_curves <- function(qsip_data_object,
                                colors = NULL,
                                title = NULL) {
 
-  stopifnot("sample_data should be class <qsip_data>" = "qsip_data" %in% class(qsip_data))
+  is_qsip_data(qsip_data_object, error = TRUE)
+
+  # error if title is not a string
+  if (!is.null(title) && !is.character(title)) {
+    stop("title must be a character string", call. = FALSE)
+  }
+
 
   # bind variables
   sample_id <- gradient_position <- source_mat_id <- isotope <- WAD <- gradient_pos_density <- gradient_pos_rel_amt <- NULL
 
-  df <- qsip_data@tube_rel_abundance |>
+  df <- qsip_data_object@tube_rel_abundance |>
     dplyr::left_join(
-      qsip_data@sample_data@data |>
+      qsip_data_object@sample_data@data |>
         dplyr::select(sample_id, gradient_position),
       by = "sample_id"
     ) |>
     dplyr::left_join(
-      qsip_data@source_data@data |>
+      qsip_data_object@source_data@data |>
         dplyr::select(source_mat_id, isotope),
       by = "source_mat_id"
     )
@@ -38,7 +44,7 @@ plot_sample_curves <- function(qsip_data,
   df <- df |>
     dplyr::filter(gradient_position > 0)
 
-  source_wads <- qsip_data@source_wads |>
+  source_wads <- qsip_data_object@source_wads |>
     dplyr::filter(!is.na(WAD))
 
   if (is.null(colors)) {

diff --git a/R/run_comparison_groups.R b/R/run_comparison_groups.R
@@ -32,12 +32,12 @@ run_comparison_groups <- function(groups,
                                   seed = NULL,
                                   resamples = NULL) {
 
-  is_qsip_data(qsip_data_object)
+  is_qsip_data(qsip_data_object, error = TRUE)
 
   # groups dataframe should contain group, unlabeled and labeled columns, and there can be others
   required_cols <- c("group", "unlabeled", "labeled")
   if (!all(required_cols %in% colnames(groups))) {
-    stop(glue::glue("Missing required column names in groups dataframe: {setdiff(required_cols, colnames(groups))}"))
+    stop(glue::glue("Missing required column names in groups dataframe: {setdiff(required_cols, colnames(groups))}"), call. = F)
   }
 
   # groups$group column should be unique
@@ -87,7 +87,7 @@ run_comparison_groups <- function(groups,
     dplyr::pull(value)
 
   if (length(setdiff(source_mat_ids_in_groups, get_source_mat_ids(qsip_data_object))) > 0) {
-    stop("Invalid source_mat_ids in group dataframe")
+    stop("Invalid source_mat_ids in group dataframe", call. = FALSE)
   }
 
   group_list <- split(groups, groups$group)

diff --git a/R/run_growth_calculations.R b/R/run_growth_calculations.R
@@ -50,7 +50,17 @@ get_N_total_it <- function(qsip_data_object,
     stop(glue::glue("no source_mat_ids with a 't = {t}' timepoint were found in <qsip_data>"), call. = FALSE)
   }
 
-  N_total_i0 = N_total_i0|>
+  # group can be NULL, or should be a column in N_total_i0
+  if (!is.null(group)) {
+
+     if (!group %in% colnames(N_total_i0)) {
+      stop(glue::glue("grouping variable {group} not found in source_data"), call. = FALSE)
+     }
+  }
+
+
+
+  N_total_i0 = N_total_i0 |>
     dplyr::filter(timepoint == t) |>
     dplyr::mutate(N_total_i0 = REL * total_abundance)
     # dplyr::select(feature_id, source_mat_id, timepoint, N_total_i0) |>

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -120,7 +120,6 @@ reference:
   - calculate_di
   - calculate_bi
   - plot_resampling_convergence
-  - isotope_palette
   - jgi_mixes
 
 articles:

diff --git a/tests/testthat/_snaps/get_N_total_it.md b/tests/testthat/_snaps/get_N_total_it.md
@@ -23,3 +23,28 @@
       10 taxon_10      2793486.          0
       # i 354 more rows
 
+# works with grouping
+
+    Code
+      get_N_total_it(example_qsip_growth_object, t = 0, group = "isotopolog")
+    Condition
+      Warning:
+      1 feature_ids have zero abundance at time 0:
+      Warning:
+      taxon_194
+    Output
+      # A tibble: 364 x 4
+         feature_id isotopolog  N_total_i0 timepoint1
+         <chr>      <chr>            <dbl>      <dbl>
+       1 taxon_1    water      1595472105.          0
+       2 taxon_2    water        64576684.          0
+       3 taxon_3    water         4488930.          0
+       4 taxon_4    water         2494463.          0
+       5 taxon_5    water         9849881.          0
+       6 taxon_6    water       697760597.          0
+       7 taxon_7    water         4702904.          0
+       8 taxon_8    water       224366766.          0
+       9 taxon_9    water         1386539.          0
+      10 taxon_10   water         2793486.          0
+      # i 354 more rows
+