Added ggplot2 capabilities

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: toxpiR
 Type: Package
 Title: Create ToxPi Prioritization Models
-Version: 1.2.1
+Version: 1.3.0
 Authors@R: 
     c(person("Dayne L", "Filer", 
              role = c("aut", "cre", "fnd"), 
@@ -14,6 +14,8 @@ Authors@R:
              comment = c(ORCID = "0000-0001-5447-0129")),
       person("Skylar W", "Marvel",
              role = "aut"),
+      person("Jonathon", "Fleming",
+             role = "aut"),
       person("Alison A", "Motsinger-Reif",
              role = c("fnd"),
              comment = c(ORCID = "0000-0003-1346-2493")),
@@ -41,10 +43,11 @@ Imports:
     BiocGenerics,
     pryr,
     tidyr,
-    utils
+    utils,
+    ggplot2
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Depends: 
     R (>= 4.0)

NAMESPACE

@@ -44,6 +44,7 @@ exportMethods(plot)
 exportMethods(sort)
 exportMethods(txpCalculateScores)
 exportMethods(txpIDs)
+exportMethods(txpMissing)
 exportMethods(txpModel)
 exportMethods(txpRanks)
 exportMethods(txpResultParam)
@@ -53,6 +54,7 @@ exportMethods(txpSlices)
 exportMethods(txpTransFuncs)
 exportMethods(txpValueNames)
 exportMethods(txpWeights)
+import(ggplot2)
 import(grid)
 import(methods)
 importClassesFrom(S4Vectors,List)

R/allClasses.R

@@ -33,8 +33,8 @@ setClassUnion("TxpTransFunc_OR_NULL", members = c("TxpTransFunc", "NULL"))
 #' @rdname TxpTransFuncList-class
 #' @exportClass TxpTransFuncList
 
-setClass("TxpTransFuncList", 
-         contains = "SimpleList", 
+setClass("TxpTransFuncList",
+         contains = "SimpleList",
          prototype = prototype(elementType = "TxpTransFunc_OR_NULL"))
 
 ##----------------------------------------------------------------------------##
@@ -43,7 +43,7 @@ setClass("TxpTransFuncList",
 #' @rdname TxpSlice-class
 #' @exportClass TxpSlice
 
-setClass("TxpSlice", 
+setClass("TxpSlice",
          slots = c(txpValueNames = "character",
                    txpTransFuncs = "TxpTransFuncList"))
 
@@ -66,8 +66,8 @@ setClass("TxpSliceList",
 #' @rdname TxpModel-class
 #' @exportClass TxpModel
 
-setClass("TxpModel", 
-         slots = c(txpSlices = "TxpSliceList", 
+setClass("TxpModel",
+         slots = c(txpSlices = "TxpSliceList",
                    txpWeights = "numeric",
                    txpTransFuncs = "TxpTransFuncList"))
 
@@ -90,8 +90,8 @@ setClass("TxpModelList",
 #' @name TxpResultParam-class
 #' @exportClass TxpResultParam
 
-setClass("TxpResultParam", 
-         slots = c(rank.ties.method = "character", 
+setClass("TxpResultParam",
+         slots = c(rank.ties.method = "character",
                    negative.value.handling = "character"))
 
 ##----------------------------------------------------------------------------##
@@ -100,10 +100,11 @@ setClass("TxpResultParam",
 #' @name TxpResult-class
 #' @exportClass TxpResult
 
-setClass("TxpResult", 
-         slots = c(txpScores = "numeric", 
+setClass("TxpResult",
+         slots = c(txpScores = "numeric",
                    txpSliceScores = "matrix",
                    txpRanks = "numeric",
+                   txpMissing = "numeric",
                    txpModel = "TxpModel",
                    txpIDs = "character_OR_NULL",
                    txpResultParam = "TxpResultParam"))

R/allGenerics.R

@@ -5,12 +5,12 @@
 
 #' @name txpGenerics
 #' @title toxpiR package generics
-#' @description toxpiR package generics; see class man pages for associated 
+#' @description toxpiR package generics; see class man pages for associated
 #' methods
 #' @param x toxpiR S4 object
 #' @param value Replacement value
 #' @param ... Included for extendability; not currently used
-#' 
+#'
 #' @return See specific methods for details.
 
 NULL
@@ -19,32 +19,32 @@ NULL
 setGeneric("txpValueNames", function(x, ...) standardGeneric("txpValueNames"))
 
 #' @rdname txpGenerics
-setGeneric("txpValueNames<-", 
+setGeneric("txpValueNames<-",
            function(x, ..., value) standardGeneric("txpValueNames<-"))
 
 #' @rdname txpGenerics
 setGeneric("txpTransFuncs", function(x, ...) standardGeneric("txpTransFuncs"))
 
 #' @rdname txpGenerics
-setGeneric("txpTransFuncs<-", 
+setGeneric("txpTransFuncs<-",
            function(x, ..., value) standardGeneric("txpTransFuncs<-"))
 
 #' @rdname txpGenerics
 setGeneric("txpSlices", function(x, ...) standardGeneric("txpSlices"))
 
 #' @rdname txpGenerics
-setGeneric("txpSlices<-", 
+setGeneric("txpSlices<-",
            function(x, ..., value) standardGeneric("txpSlices<-"))
 
 #' @rdname txpGenerics
 setGeneric("txpWeights", function(x, ...) standardGeneric("txpWeights"))
 
 #' @rdname txpGenerics
-setGeneric("txpWeights<-", 
+setGeneric("txpWeights<-",
            function(x, ..., value) standardGeneric("txpWeights<-"))
 
 #' @rdname txpCalculateScores
-setGeneric("txpCalculateScores", 
+setGeneric("txpCalculateScores",
            function(model, input, ...) standardGeneric("txpCalculateScores"))
 
 #' @rdname txpGenerics
@@ -65,5 +65,8 @@ setGeneric("txpIDs<-", function(x, ..., value) standardGeneric("txpIDs<-"))
 #' @rdname txpGenerics
 setGeneric("txpRanks", function(x, ...) standardGeneric("txpRanks"))
 
+#' @rdname txpGenerics
+setGeneric("txpMissing", function(x, ...) standardGeneric("txpMissing"))
+
 #' @rdname txpGenerics
 setGeneric("txpResultParam", function(x, ...) standardGeneric("txpResultParam"))