adeschen
diff --git a/‎NAMESPACE
Lines changed: 5 additions & 0 deletions b/‎NAMESPACE
Lines changed: 5 additions & 0 deletions
diff --git a/‎R/OrganoidsToolBox.R
Lines changed: 53 additions & 0 deletions b/‎R/OrganoidsToolBox.R
Lines changed: 53 additions & 0 deletions
@@ -4,16 +4,21 @@ S3method(is,DrugAUCQuantile)
 export(plotDrugAUCDensityCurve)
 export(plotDrugAUCViolinPlot)
 export(selectOrgForOneDrug)
+export(selectOrgWithoutReplicateForOneDrug)
 importFrom(S4Vectors,isSingleNumber)
 importFrom(ggplot2,.data)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,element_line)
 importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_density)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_rug)
 importFrom(ggplot2,geom_violin)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,position_jitter)
 importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_fill_manual)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
 importFrom(ggplot2,xlab)
 
@@ -208,3 +208,56 @@ NULL
 #'
 #'
 NULL
+
+
+#' Simple demo patient information dataset. The information is related to the
+#' organoids present in the 'drugScreening' dataset.
+#'
+#' @name patientInfo
+#'
+#' @docType data
+#'
+#' @aliases patientInfo
+#'
+#' @format a \code{data.frame} with the following columns:
+#' \itemize{
+#' \item \code{organoid_id} { a \code{character} string representing the
+#' organoid identifier. }
+#' \item \code{patient_id} { a \code{character} string representing the patient
+#' identifier. }
+#' }
+#'
+#' @seealso
+#' \itemize{
+#' \item \code{\link{selectOrgForOneDrug}} { for selecting the organoids
+#' with sensitive and resistant behavior for a
+#' specific drug screening.}
+#' \item \code{\link{selectOrgWithoutReplicateForOneDrug}} { for selecting
+#' the unrelated organoids (only one organoid per patient)
+#' with sensitive and resistant behavior for a
+#' specific drug screening.}
+#' }
+#'
+#' @usage data(drugScreening)
+#'
+#' @keywords datasets
+#'
+#' @examples
+#'
+#' ## Load drug screen dataset for 1 drug
+#' data(drugScreening)
+#'
+#' ## Load patient information dataset for 1 drug
+#' data(patientInfo)
+#'
+#' ## Calculate the extreme organoids for the methotrexate drug screening
+#' ## using a quantile of 1/3
+#' results <- selectOrgWithoutReplicateForOneDrug(drugScreening=drugScreening,
+#'     drugName="Methotrexate", study="MEGA-TEST", screenType="TEST-01",
+#'     patientInfo=patientInfo, doseType="Averaged", quantile=1/4)
+#'
+#' ## The information of the extreme organoids is found it the 'extreme' entry
+#' results$extreme
+#'
+#'
+NULL