v0.17.10

jeffkimbrel · Nov 8, 2024 · 05cc6f7 · 05cc6f7
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commit 05cc6f7
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Showing 13 changed files with 35 additions and 39 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.17.9
+Version: 0.17.10
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7213-9392"))

diff --git a/R/add_taxonomy.R b/R/add_taxonomy.R
@@ -19,7 +19,7 @@
 #'
 #' @returns An updated `qsip_feature_data` with the taxonomy slot populated with a taxonomy dataframe.
 #' @importFrom rlang :=
-#'
+
 add_taxonomy <- function(feature_object, taxa, feature_id) {
 
   # make sure feature_object is the right type

diff --git a/R/plot_filter_results.R b/R/plot_filter_results.R
@@ -10,7 +10,6 @@
 #'
 #' @param qsip_data_object (*qsip_data*)
 #' @param return_type (*string, default: combined*) Changes the return type from a combined plot (*combined*), list of individual plots (*individual*) or list of dataframes (*dataframe*)
-#' @param colors (*strings*) An optional color palette
 #'
 #' @export
 #'
@@ -21,28 +20,26 @@
 
 plot_filter_results <- function(qsip_data_object,
                                 return_type = "combined",
-                                colors = NULL) {
-  stopifnot("qsip_data_object should be class <qsip_data>" = "qsip_data" %in% class(qsip_data_object))
+                                colors = lifecycle::deprecated()) {
 
-  if (!return_type %in% c("combined", "individual", "dataframe")) {
-    stop(glue::glue("return_type should be either one of 'combined', 'individual' or 'dataframe'"))
+  is_qsip_filtered(qsip_data_object, error = TRUE)
+
+  if (lifecycle::is_present(colors)) {
+    lifecycle::deprecate_warn("0.17.10", "plot_filter_results(colors)")
   }
 
-  if (length(qsip_data_object@filter_results) == 0) {
-    stop(glue::glue("please run run_filter_feature() on qsip_data_object before plotting results"))
+  if (!return_type %in% c("combined", "individual", "dataframe")) {
+    stop(glue::glue("return_type should be either one of 'combined', 'individual' or 'dataframe'"))
   }
 
   # bind variables
   source_mat_id <- fraction_call <- tube_rel_abundance <- n <- NULL
 
-  if (is.null(colors)) {
-    colors <- c(
-      "Fraction Passed" = "#2B92BE",
-      "Fraction Filtered" = "#BE572B",
-      "Zero Fractions" = "gray30"
-    )
-  }
-
+  colors <- c(
+    "Fraction Passed" = "#037bcf",
+    "Fraction Filtered" = "#BE572B",
+    "Zero Fractions" = "gray70"
+  )
 
   by_abundance_df <- qsip_data_object@filter_results$fraction_filtered |>
     dplyr::group_by(source_mat_id, fraction_call) |>

diff --git a/R/qsip_objects.R b/R/qsip_objects.R
@@ -595,19 +595,19 @@ S7::method(get_dataframe, qsip_data) <- function(x, type, original_headers = FAL
 
 S7::method(print, qsip_source_data) <- function(x, ...) {
   sd = x@data
-  print(glue::glue_col("<qSIP2::qsip_source_data>
+  print(glue::glue_col("<qsip_source_data>
                        source_material_id count: {green {length(unique(sd$source_mat_id))}}"))
 }
 
 S7::method(print, qsip_sample_data) <- function(x, ...) {
   sd = x@data
-  print(glue::glue_col("<qSIP2::qsip_sample_data>
+  print(glue::glue_col("<qsip_sample_data>
                        source_material_id count: {green {length(unique(sd$source_mat_id))}}
                        sample_id count: {green {length(unique(sd$sample_id))}}"))
 }
 
 S7::method(print, qsip_feature_data) <- function(x, ...) {
-  print(glue::glue_col("<qSIP2::qsip_feature_data>
+  print(glue::glue_col("<qsip_feature_data>
                        feature_id count: {green {dim(x@data)[1]}}
                        sample_id count: {green {dim(x@data)[2] - 1}}
                        data type: {green {x@type}}"))
@@ -616,7 +616,7 @@ S7::method(print, qsip_feature_data) <- function(x, ...) {
 S7::method(print, qsip_data) <- function(x, ...) {
 
 
-  print(glue::glue_col("<qSIP2::qsip_data>
+  print(glue::glue_col("<qsip_data>
                        group: {green {ifelse(is.null(x@filter_results$group), 'none', x@filter_results$group)}}
                        feature_id count: {green {length(get_feature_ids(x, filtered = is_qsip_filtered(x)))} of {dim(x@feature_data@data)[1]}}
                        sample_id count: {green {length(unique(x@sample_data@data$sample_id))}}

diff --git a/man/plot_filter_results.Rd b/man/plot_filter_results.Rd
diff --git a/tests/testthat/_snaps/qsip_data.md b/tests/testthat/_snaps/qsip_data.md
@@ -6,7 +6,7 @@
       There are 15 source_mat_ids, and they are all shared between the source and sample objects
       There are 284 sample_ids, and they are all shared between the sample and feature objects
     Output
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: none
       feature_id count: 2030 of 2030
       sample_id count: 284

diff --git a/tests/testthat/_snaps/qsip_sample_data.md b/tests/testthat/_snaps/qsip_sample_data.md
@@ -5,7 +5,7 @@
         gradient_position = "Fraction", gradient_pos_density = "density_g_ml",
         gradient_pos_amt = "avg_16S_g_soil", gradient_pos_rel_amt = "gradient_pos_rel_amt")
     Output
-      <qSIP2::qsip_sample_data>
+      <qsip_sample_data>
       source_material_id count: 15
       sample_id count: 284
 
@@ -18,7 +18,7 @@
     Message
       <gradient_pos_rel_amt> not specified. Calculating using avg_16S_g_soil column
     Output
-      <qSIP2::qsip_sample_data>
+      <qsip_sample_data>
       source_material_id count: 15
       sample_id count: 284
 
diff --git a/tests/testthat/_snaps/run_EAF_calculations.md b/tests/testthat/_snaps/run_EAF_calculations.md
@@ -3,7 +3,7 @@
     Code
       run_EAF_calculations(qsip_normal_strict_resampled)
     Output
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: none
       feature_id count: 74 of 2030
       sample_id count: 284

diff --git a/tests/testthat/_snaps/run_comparison_groups.md b/tests/testthat/_snaps/run_comparison_groups.md
@@ -5,7 +5,7 @@
         resamples = 100)
     Output
       $Drought
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: Drought
       feature_id count: 305 of 2030
       sample_id count: 284
@@ -15,7 +15,7 @@
       growth: FALSE
       
       $Normal
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: Normal
       feature_id count: 239 of 2030
       sample_id count: 284

diff --git a/tests/testthat/_snaps/run_feature_filter.md b/tests/testthat/_snaps/run_feature_filter.md
@@ -21,7 +21,7 @@
       =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+
       In total, 257 unique feature_ids passed all fraction and source filtering requirements
     Output
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: none
       feature_id count: 257 of 2030
       sample_id count: 284

diff --git a/tests/testthat/_snaps/run_growth_calculations.md b/tests/testthat/_snaps/run_growth_calculations.md
@@ -8,7 +8,7 @@
       Warning:
       3968 resamplings have a negative EAF value or calculated labeled copy numbers less than 0. These values have been filtered out and added to @growth$negative_labeled
     Output
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: Day 10
       feature_id count: 358 of 364
       sample_id count: 106

diff --git a/tests/testthat/_snaps/run_resampling.md b/tests/testthat/_snaps/run_resampling.md
@@ -3,7 +3,7 @@
     Code
       run_resampling(qsip_normal_strict_filtered, resamples = 100, with_seed = 21)
     Output
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: none
       feature_id count: 74 of 2030
       sample_id count: 284
@@ -19,7 +19,7 @@
     Message
       Using random seed. For consistency, you can use the with_seed argument
     Output
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: none
       feature_id count: 74 of 2030
       sample_id count: 284
@@ -35,7 +35,7 @@
     Message
       Using random seed. For consistency, you can use the with_seed argument
     Output
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: none
       feature_id count: 74 of 2030
       sample_id count: 284
@@ -54,7 +54,7 @@
       Warning:
       NA unlabeled and NA labeled feature_ids had resampling failures. Run `get_resample_counts()` or `plot_successful_resamples()` on your <qsip_data> object to inspect.
     Output
-      <qSIP2::qsip_data>
+      <qsip_data>
       group: none
       feature_id count: 74 of 2030
       sample_id count: 284

diff --git a/...that/test-plot_filter_gradient_position.R → tests/testthat/test-plot_filter_results.R b/...that/test-plot_filter_gradient_position.R → tests/testthat/test-plot_filter_results.R
@@ -2,9 +2,6 @@ qsip_normal_strict_filtered <- readRDS(test_path("fixtures", "qsip_normal_strict
 
 test_that("works as expected", {
   expect_true("ggplot" %in% class(plot_filter_results(qsip_normal_strict_filtered)))
-  expect_true("ggplot" %in% class(plot_filter_results(qsip_normal_strict_filtered,
-    colors = c("red", "blue", "black")
-  )))
 
   expect_true("ggplot" %in% class(plot_filter_results(qsip_normal_strict_filtered,
     return_type = "combined"