updates main functionality to columnar samples

as well as removing all of the old correlation functionality, and all tests pass

DESCRIPTION

@@ -1,21 +1,21 @@
 Package: visualizationQualityControl
-Version: 0.4.11
+Version: 0.5.1
 Title: Development of visualization methods for quality control
 Description: Provides utilities useful quality control of
         high-throughput -omics datasets.
 Authors@R: c(person(given = c("Robert", "M"), family = "Flight", email
         = "[email protected]", role = c("aut", "cre")), person(given
         = c("Hunter", "NB"), family = "Moseley", email =
         "[email protected]", role = c("aut")))
-Date: 2021-12-28
+Date: 2024-02-15
 Depends: R (>= 3.1.1)
 biocViews:
 Imports: ComplexHeatmap (>= 1.2.1), stats, dendsort, colorspace, dplyr,
         ggplot2, broom, knitrProgressBar, magrittr, purrr
 License: MIT + file LICENSE
 VignetteBuilder: knitr
-Suggests: testthat, knitr, rmarkdown, circlize, viridis, ICIKendallTau,
-        ggforce
+Suggests: testthat, knitr, rmarkdown, circlize, viridis, ICIKendallTau
+        (>= 1.0.0), ggforce
 RoxygenNote: 7.2.3
 Encoding: UTF-8
 LinkingTo: Rcpp

NAMESPACE

@@ -4,25 +4,15 @@ export("%>%")
 export(calc_sd_rsd)
 export(calc_sd_rsd_nls)
 export(calculate_fratio)
-export(calculate_weights)
-export(correspondence)
 export(count_matching_features)
 export(determine_outliers)
 export(filter_non_zero_percentage)
 export(generate_group_colors)
-export(globally_it_weighted_pairwise_correlation)
-export(information_volume)
+export(keep_non_missing_percentage)
 export(keep_non_zero_percentage)
-export(locally_it_weighted_pairwise_correlation)
 export(median_class_correlations)
 export(median_correlations)
 export(outlier_fraction)
-export(pairwise_correlation)
-export(pairwise_correlation_both0)
-export(pairwise_correlation_counts)
-export(pairwise_correlation_multicore)
-export(pairwise_distance)
-export(pairwise_nonzero)
 export(similarity_reorder)
 export(similarity_reorderbyclass)
 export(split_groups)

NEWS.md

@@ -1,4 +1,15 @@
-# vsualizationQualityControl 0.4.11
+# visualizationQualityControl 0.5.0
+
+* Changed some functions to treat columns as samples and rows as features:
+  * `keep_non_zero_percentage`
+  * `summarize_data`
+  * `calculate_fratio`
+
+* Added `keep_non_missing_percentage`, which allows using multiple values to represent missingnes.
+* Made `summarize_data` handle possible missing values.
+* Removed correlation calculation functions, those have been superseded by [ICIKendallTau](https://moseleybioinformaticslab.github.io/ICIKendallTau/).
+
+# visualizationQualityControl 0.4.11
 
 * Added a new argument `only_high` to `determine_outliers` to only look at the high end of the score distribution for outliers, as sometimes `boxplot.stats` will pick up outliers at the low end as well.