Improves mutually_exclusive() example

Adds demonstration of CSV support for the quality_opposites paramter to mutually_exclusive(). Fixes #271
phenoscape · Nov 9, 2022 · 2c1d347 · 2c1d347
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diff --git a/R/mutual_exclusivity.R b/R/mutual_exclusivity.R
@@ -311,6 +311,12 @@ find_quality_opposites <- function(phenotype_quality, quality_opposites) {
 #' # compare the phenotypes using opposite quality data
 #' exclusivity <- mutually_exclusive(phenotypes_to_compare, quality_opposites=quality_opposites)
 #' exclusivity$dataframe$mutual_exclusivity
+#'
+#' # compare the phenotypes using opposites from a csv file with "quality.a" and "quality.b" columns
+#' opposites_csv_path <- system.file("examples", "opposites.csv", package = "rphenoscape")
+#' quality_opposites <- read.csv(opposites_csv_path)
+#' exclusivity <- mutually_exclusive(phenotypes_to_compare, quality_opposites=quality_opposites)
+#' exclusivity$dataframe$mutual_exclusivity
 #' @export
 mutually_exclusive <- function(phenotypes, studies=NULL, progress_bar=FALSE, quality_opposites=NULL){
 

diff --git a/inst/examples/opposites.csv b/inst/examples/opposites.csv
@@ -0,0 +1,2 @@
+quality.a,quality.b
+http://purl.obolibrary.org/obo/PATO_0001154,http://purl.obolibrary.org/obo/PATO_0000574
diff --git a/man/mutually_exclusive.Rd b/man/mutually_exclusive.Rd
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		quality.a,quality.b
		http://purl.obolibrary.org/obo/PATO_0001154,http://purl.obolibrary.org/obo/PATO_0000574