changed name for new option, because its by scores, not just correlation

MoseleyBioinformaticsLab · Jul 13, 2023 · a5e2e71 · a5e2e71
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Showing 7 changed files with 11 additions and 11 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,6 @@
 # vsualizationQualityControl 0.4.11
 
-* Added a new argument `only_low` to `determine_outliers` to only look at the low end of the score distribution for outliers, as sometimes `boxplot.stats` will pick up outliers at the high end as well.
+* 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.
 
 # visualizationQualityControl 0.4.10
 

diff --git a/R/correlations.R b/R/correlations.R
@@ -812,7 +812,7 @@ outlier_fraction <- function(data, sample_classes = NULL, n_trim = 3,
 #' @param outlier_fraction outlier fractions
 #' @param cor_weight how much weight for the correlation score?
 #' @param frac_weight how much weight for the outlier fraction?
-#' @param only_low should only things at the low end of score be removed?
+#' @param only_high should only things at the low end of score be removed?
 #' 
 #' @details For outlier sample detection, one should 
 #'   first generate median correlations using
@@ -827,7 +827,7 @@ outlier_fraction <- function(data, sample_classes = NULL, n_trim = 3,
 #' @export
 #' @return data.frame
 determine_outliers = function(median_correlations = NULL, outlier_fraction = NULL,
-                              cor_weight = 1, frac_weight = 1, only_low = TRUE){
+                              cor_weight = 1, frac_weight = 1, only_high = TRUE){
 
   if (!is.null(median_correlations) && !is.null(outlier_fraction)) {
     full_data = dplyr::left_join(median_correlations, outlier_fraction, by = "sample_id", suffix = c(".cor", ".frac"))
@@ -867,7 +867,7 @@ determine_outliers = function(median_correlations = NULL, outlier_fraction = NUL
   full_data$outlier = FALSE
   full_data$outlier[full_data$sample_id %in% all_out] = TRUE
 
-  if (only_low) {
+  if (only_high) {
     split_data = split(full_data, full_data$sample_class)
     full_data = purrr::map(split_data, \(in_data){
       mean_score = mean(in_data$score)

diff --git a/docs/articles/quality_control.html b/docs/articles/quality_control.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   pca_testing: pca_testing.html
   quality_control: quality_control.html
-last_built: 2023-07-13T00:03Z
+last_built: 2023-07-13T01:05Z
 
diff --git a/docs/reference/determine_outliers.html b/docs/reference/determine_outliers.html
diff --git a/docs/search.json b/docs/search.json
diff --git a/man/determine_outliers.Rd b/man/determine_outliers.Rd