@@ -38,6 +38,8 @@ export(modify)

 export(pileupToCoverage)

 export(plotCompare)

 export(plotCompareByCoord)

+export(plotData)

+export(plotDataByCoord)

 export(plotROC)

 export(replicates)

 export(sequenceData)

@@ -46,8 +48,6 @@ export(settings)

 export(subsetByCoord)

 export(validAggregate)

 export(validModification)

-export(visualizeData)

-export(visualizeDataByCoord)

 exportClasses(CoverageSequenceData)

 exportClasses(End3SequenceData)

 exportClasses(End5SequenceData)

@@ -89,6 +89,8 @@ exportMethods(modify)

 exportMethods(names)

 exportMethods(pileupToCoverage)

 exportMethods(plotCompareByCoord)

+exportMethods(plotData)

+exportMethods(plotDataByCoord)

 exportMethods(plotROC)

 exportMethods(ranges)

 exportMethods(replicates)

@@ -99,8 +101,6 @@ exportMethods(settings)

 exportMethods(subsetByCoord)

 exportMethods(validAggregate)

 exportMethods(validModification)

-exportMethods(visualizeData)

-exportMethods(visualizeDataByCoord)

 import(GenomicRanges)

 import(Gviz)

 import(S4Vectors)

@@ -16,7 +16,7 @@ NULL

 #' @export

 setGeneric( 

   name = "plotROC",

-  signature = c("x"),

+  signature = "x",

   def = function(x, coord, ...)

     standardGeneric("plotROC")

 )

@@ -81,35 +81,35 @@ setGeneric(

 #' @rdname Modifier-functions

 #' @export

 setGeneric( 

-  name = "settings",

-  def = function(x, name = NULL) standardGeneric("settings")

+  name = "validAggregate",

+  def = function(x) standardGeneric("validAggregate")

 )

 #' @rdname Modifier-functions

 #' @export

 setGeneric( 

-  name = "settings<-",

-  def = function(x, name, value) standardGeneric("settings<-")

+  name = "validModification",

+  def = function(x) standardGeneric("validModification")

 )

-#' @rdname Modifier-functions

+

+#' @rdname settings

 #' @export

 setGeneric( 

-  name = "validAggregate",

-  def = function(x) standardGeneric("validAggregate")

+  name = "settings",

+  def = function(x, name = NULL) standardGeneric("settings")

 )

-#' @rdname Modifier-functions

+#' @rdname settings

 #' @export

 setGeneric( 

-  name = "validModification",

-  def = function(x) standardGeneric("validModification")

+  name = "settings<-",

+  def = function(x, name, value) standardGeneric("settings<-")

 )

-

 # Modifier/ModifierSet functions -----------------------------------------------

 #' @rdname modify

 #' @export

 setGeneric( 

   name = "modify",

-  signature = c("x"),

+  signature = "x",

   def = function(x, ...) standardGeneric("modify")

 )

@@ -117,7 +117,7 @@ setGeneric(

 #' @export

 setGeneric( 

   name = "findMod",

-  signature = c("x"),

+  signature = "x",

   def = function(x) standardGeneric("findMod")

 )

@@ -128,7 +128,7 @@ setGeneric(

 #' @export

 setGeneric( 

   name = "aggregate",

-  signature = c("x"),

+  signature = "x",

   def = function(x, ...) standardGeneric("aggregate")

 )

 #' @rdname aggregate

@@ -141,14 +141,14 @@ setGeneric(

 #' @export

 setGeneric( 

   name = "getAggregateData",

-  signature = c("x"),

+  signature = "x",

   def = function(x) standardGeneric("getAggregateData")

 )

 #' @rdname aggregate

 #' @export

 setGeneric( 

   name = "hasAggregateData",

-  signature = c("x"),

+  signature = "x",

   def = function(x) standardGeneric("hasAggregateData")

 ) 

@@ -170,27 +170,27 @@ setGeneric(

   def = function(x, coord, ...)

     standardGeneric("labelByCoord")

 )

-#' @rdname visualizeData

+#' @rdname plotData

 #' @export

 setGeneric(

-  name = "visualizeData",

-  signature = c("x"),

+  name = "plotData",

+  signature = "x",

   def = function(x, name, from = 1L, to = 30L, type, ...)

-    standardGeneric("visualizeData")

+    standardGeneric("plotData")

 )

-#' @rdname visualizeData

+#' @rdname plotData

 #' @export

 setGeneric(

-  name = "visualizeDataByCoord",

+  name = "plotDataByCoord",

   signature = c("x","coord"),

   def = function(x, coord, type, window.size = 15L, ...)

-    standardGeneric("visualizeDataByCoord")

+    standardGeneric("plotDataByCoord")

 )

-#' @rdname visualizeData

+#' @rdname plotData

 #' @export

 setGeneric(

   name = "getDataTrack",

-  signature = c("x"),

+  signature = "x",

   def = function(x, name, ...)

     standardGeneric("getDataTrack")

 )

@@ -201,7 +201,7 @@ setGeneric(

 #' @export

 setGeneric( 

   name = "compare",

-  signature = c("x"),

+  signature = "x",

   def = function(x, name, from = 1L, to = 30L, ...)

     standardGeneric("compare")

 ) 

@@ -217,7 +217,7 @@ setGeneric(

 #' @export

 setGeneric( 

   name = "plotCompare",

-  signature = c("x"),

+  signature = "x",

   def = function(x, name, from = 1L, to = 30L, normalize, ...)

     standardGeneric("plotCompare")

 ) 

@@ -105,10 +105,10 @@ NULL

 #' see also the man pages for the functions mentioned below.

 #' @param value See \code{\link[RNAmodR:Modifier-functions]{settings}}

 #' @param coord,name,from,to,type,window.size,... See 

-#' \code{\link{visualizeData}}

+#' \code{\link{plotData}}

 #' 

 #' @details 

-#' \code{ModInosine} specific arguments for \link{visualizeData}:

+#' \code{ModInosine} specific arguments for \link{plotData}:

 #' \itemize{

 #' \item{\code{colour.bases} - }{a named character vector of \code{length = 4} 

 #' for the colours of the individual bases. The names are expected to be 

@@ -122,9 +122,9 @@ NULL

 #' \item{\code{modify}} {See \code{\link{modify}}.}

 #' \item{\code{getDataTrack}} {a list of 

 #' \code{\link[Gviz:DataTrack-class]{DataTrack}} objects. See 

-#' \code{\link{visualizeDataByCoord}}.}

-#' \item{\code{visualizeData}} {See \code{\link{visualizeDataByCoord}}.}

-#' \item{\code{visualizeDataByCoord}} {See \code{\link{visualizeDataByCoord}}.}

+#' \code{\link{plotDataByCoord}}.}

+#' \item{\code{plotData}} {See \code{\link{plotDataByCoord}}.}

+#' \item{\code{plotDataByCoord}} {See \code{\link{plotDataByCoord}}.}

 #' }

 #' 

 #' @examples 

@@ -227,7 +227,7 @@ setMethod(f = "aggregateData",

 .find_inosine <- function(x){

   if(!hasAggregateData(x)){

-    stop("Something went wrong.")

+    stop("")

   }

   letters <- IRanges::CharacterList(strsplit(as.character(sequences(x)),""))

   # get the aggregate data

@@ -243,7 +243,7 @@ setMethod(f = "aggregateData",

   # find inosine positions by looking for A to G conversion at position with 

   # enough coverage

   grl <- ranges(x)

-  modifications <- mapply(

+  modifications <- Map(

     function(m,c,l,r){

       m <- m[l == "A" &

                m$score >= minScore & 

@@ -257,19 +257,17 @@ setMethod(f = "aggregateData",

     mod,

     coverage,

     letters,

-    grl,

-    SIMPLIFY = FALSE)

+    grl)

   f <- !vapply(modifications,

                is.null,

                logical(1))

-  modifications <- mapply(

+  modifications <- Map(

     function(m,name){

       m$Parent <- name

       m

     },

     modifications[f],

-    names(grl)[f],

-    SIMPLIFY = FALSE)

+    names(grl)[f])

   modifications <- GenomicRanges::GRangesList(modifications)

   unname(unlist(modifications))

 }

@@ -2,10 +2,10 @@

 #' @include Modifier-Inosine-class.R

 NULL

-RNAMODR_I_PLOT_DATA <- c("score")

-RNAMODR_I_PLOT_DATA_DEFAULT <- c("score")

+RNAMODR_I_PLOT_DATA <- "score"

+RNAMODR_I_PLOT_DATA_DEFAULT <- "score"

-RNAMODR_I_PLOT_DATA_COLOURS <- c("score" = "#ABABAB") 

+RNAMODR_I_PLOT_DATA_COLOURS <- c(score = "#ABABAB") 

 RNAMODR_I_PLOT_DATA_NAMES <- c(score = "Score Inosine")

 .norm_viz_mod_inosine_args <- function(input, type){

@@ -66,7 +66,7 @@ setMethod(

 #' @rdname ModInosine-functions

 #' @export

 setMethod(

-  f = "visualizeDataByCoord",

+  f = "plotDataByCoord",

   signature = signature(x = "ModInosine", coord = "GRanges"),

   definition = function(x, coord, type = "score", window.size = 15L, ...) {

     if(missing(type)){

@@ -80,7 +80,7 @@ setMethod(

 #' @rdname ModInosine-functions

 #' @export

 setMethod(

-  f = "visualizeData",

+  f = "plotData",

   signature = signature(x = "ModInosine"),

   definition = function(x, name, from, to, type = "score", ...) {

     if(missing(type)){

@@ -94,7 +94,7 @@ setMethod(

 #' @rdname ModInosine-functions

 #' @export

 setMethod(

-  f = "visualizeDataByCoord",

+  f = "plotDataByCoord",

   signature = signature(x = "ModSetInosine", coord = "GRanges"),

   definition = function(x, coord, type = "score", window.size = 15L, ...) {

     if(missing(type)){

@@ -108,7 +108,7 @@ setMethod(

 #' @rdname ModInosine-functions

 #' @export

 setMethod(

-  f = "visualizeData",

+  f = "plotData",

   signature = signature(x = "ModSetInosine"),

   definition = function(x, name, from, to, type = "score", ...) {

     if(missing(type)){

@@ -5,6 +5,10 @@

 #' @include Modifier-utils.R

 NULL

+invalidMessage <- paste0("Settings were changed after data aggregation or ",

+                         "modification search. Rerun with modify(x,force = ",

+                         "TRUE) to update with current settings.")

+

 #' @name Modifier-class

 #' @aliases Modifier

 #'

@@ -61,6 +65,11 @@ NULL

 #' For this example a \code{list} of \code{character} vectors is expected.

 #' Each element must be named according to the names of \code{dataType()} and

 #' contain a \code{character} vector for creating a \code{SequenceData} object.

+#' 

+#' All additional options must be named and will be passed to the

+#' \code{\link[=settings]{settings}} function and onto the \code{SequenceData}

+#' objects, if \code{x} is not a \code{SequenceData} object or a list of

+#' \code{SequenceData} objects.

 #'

 #' @param className The name of the class which should be constructed.

 #' @param x the input which can be of the following types

@@ -89,10 +98,12 @@ NULL

 #' \item{\code{find.mod}:} {\code{TRUE} or \code{FALSE}: should the search for

 #' for modifications be triggered upon construction? If not the search can be

 #' started by calling the \code{modify()} function.}

+#' \item{additional parameters depending on the specific \code{Modifier} class}

 #' }

-#' All other arguments will be passed onto the \code{SequenceData} objects, if

-#' \code{x} is not a \code{SequenceData} object or a list of \code{SequenceData}

-#' objects.

+#' All additional options must be named and will be passed to the

+#' \code{\link[=settings]{settings}} function and onto the \code{SequenceData}

+#' objects, if \code{x} is not a \code{SequenceData} object or a list of

+#' \code{SequenceData} objects.

 #'

 #' @slot mod a \code{character} value, which needs to contain one or more

 #' elements from the alphabet of a

@@ -125,10 +136,13 @@ NULL

 #' @description

 #' For the \code{Modifier} and  \code{ModifierSet} classes a number of functions

 #' are implemented to access the data stored by the object.

+#' 

+#' The \code{validAggregate} and \code{validModification} functions check if

+#' \code{\link[=settings]{settings}} have been modified, after the data was 

+#' loaded. This potentially invalidates them. To update the data, run the

+#' \code{aggregate} or the \code{modify} function.

 #'

 #' @param x,object a \code{Modifier} or \code{ModifierSet} class

-#' @param name For \code{settings}: name of the setting to be returned or set

-#' @param value For \code{settings}: value of the setting to be set

 #' @param modified For \code{sequences}: \code{TRUE} or \code{FALSE}: Should

 #' the sequences be returned as a \code{ModRNAString} with the found

 #' modifications added on top of the \code{RNAString}? See

@@ -142,7 +156,6 @@ NULL

 #' \item{\code{modifierType}:} {a character vector with the appropriate class

 #' Name of a \code{\link[=Modifier-class]{Modifier}}.}

 #' \item{\code{mainScore}:} {a character vector.}

-#' \item{\code{settings}:} {a \code{Seqinfo} object.}

 #' \item{\code{sequenceData}:} {a \code{SequenceData} object.}

 #' \item{\code{modifications}:} {a \code{GRanges} or \code{GRangesList} object

 #' describing the found modifications.}

@@ -151,7 +164,13 @@ NULL

 #' \item{\code{ranges}:} {a \code{GRangesList} object with each element per

 #' transcript.}

 #' \item{\code{bamfiles}:} {a \code{BamFileList} object.}

+#' \item{\code{validAggregate}:} {\code{TRUE} or \code{FALSE}. Checks if current

+#' settings are the same for which the data was aggregate}

+#' \item{\code{validModification}:} {\code{TRUE} or \code{FALSE}. Checks if 

+#' current settings are the same for which modification were found}

 #' }

+#' 

+#' @seealso \code{\link[=settings]{settings}}

 #'

 #' @examples

 #' data(msi,package="RNAmodR")

@@ -159,7 +178,6 @@ NULL

 #' modifierType(mi) # The class name of the Modifier object

 #' modifierType(msi) #

 #' mainScore(mi)

-#' settings(mi)

 #' sequenceData(mi)

 #' modifications(mi)

 #' # general accessors

@@ -196,18 +214,18 @@ setClass("Modifier",

 # validity ---------------------------------------------------------------------

-.check_SequenceData_elements <- function(x, list){

-  if(is(list,"SequenceData")){

-    list <- list(list)

-  } else if(is(list,"list")){

-    elementTypeMatch <- !vapply(list,is,logical(1),"SequenceData")

+.check_SequenceData_elements <- function(x, data){

+  if(is(data,"SequenceData")){

+    data <- list(data)

+  } else if(is(data,"list")){

+    elementTypeMatch <- !vapply(data,is,logical(1),"SequenceData")

     if(any(elementTypeMatch)){

       stop("Not all elements are 'SequenceData' objects.", call. = FALSE)

     }

-  } else if(!is(list,"SequenceDataSet")){

-   stop("Something went wrong.")

+  } else if(!is(data,"SequenceDataSet")){

+    stop("")

   }

-  elementTypes <- vapply(list,class,character(1))

+  elementTypes <- vapply(data,class,character(1))

   if(length(elementTypes) != length(dataType(x))){

     stop("Number of 'SequenceData' elements does not match the requirements of",

          " ",class(x),". '",paste(dataType(x), collapse = "','"),"' are ",

@@ -222,8 +240,8 @@ setClass("Modifier",

   NULL

 }

-.check_SequenceDataList_data_elements <- function(x, list){

-  ans <- lapply(list, .check_SequenceData_elements, x)

+.check_SequenceDataList_data_elements <- function(x, data){

+  ans <- lapply(data, .check_SequenceData_elements, x)

   if(all(vapply(ans,is.null))) {

     return(NULL)

   }

@@ -296,9 +314,9 @@ S4Vectors::setValidity2(Class = "Modifier", .valid_Modifier)

                        settings[,f,drop = FALSE]

                      })

   if(is.null(rownames(settings[[1]]))){

-    names <- rep(" ",nrow(settings[[1]]))

+    setting_names <- rep(" ",nrow(settings[[1]]))

   } else {

-    names <- rownames(settings[[1]])

+    setting_names <- rownames(settings[[1]])

   }

   for(i in seq_along(settings)){

     out <-

@@ -312,7 +330,7 @@ S4Vectors::setValidity2(Class = "Modifier", .valid_Modifier)

       }), use.names = FALSE), nrow = 1,

       dimnames = list("", colnames(out)))

     out <- rbind(classinfo, out)

-    rownames(out) <- c(" ",names)

+    rownames(out) <- c(" ",setting_names)

     print(out, quote = FALSE, right = TRUE)

   }

 }

@@ -347,9 +365,7 @@ setMethod(

     .show_settings(settings)

     valid <- c(validAggregate(object), validModification(object))

     if(!all(valid)){

-      warning("Settings were changed after data aggregation or modification ",

-              "search. Rerun with modify(x,force = TRUE) to update with ",

-              "current settings.", call. = FALSE)

+      warning(invalidMessage, call. = FALSE)

     }

   }

 )

@@ -404,6 +420,10 @@ setMethod(f = "modifications",

               if(!assertive::is_a_bool(perTranscript)){

                 stop("'perTranscript' has to be a single logical value.")

               }

+              valid <- c(validAggregate(x), validModification(x))

+              if(!all(valid)){

+                warning(invalidMessage, call. = FALSE)

+              }

               if(perTranscript){

                 return(.get_modifications_per_transcript(x))

               }

@@ -457,7 +477,7 @@ setMethod(f = "sequences",

                 stop("'modified' has to be a single logical value.",

                      call. = FALSE)

               }

-              if(modified == FALSE){

+              if(!modified){

                 return(sequences(sequenceData(x)))

               }

               mod <- .get_modifications_per_transcript(x)

@@ -511,6 +531,59 @@ setMethod(f = "seqinfo",

 #' @rdname Modifier-functions

 #' @export

+setMethod(f = "validAggregate",

+          signature = signature(x = "Modifier"),

+          definition = function(x) x@aggregateValidForCurrentArguments

+)

+#' @rdname Modifier-functions

+#' @export

+setMethod(f = "validModification",

+          signature = signature(x = "Modifier"),

+          definition = function(x) x@modificationsValidForCurrentArguments

+)

+

+# settings ---------------------------------------------------------------------

+

+#' @name settings

+#' 

+#' @title Settings for \code{Modifier} objects

+#' 

+#' @description 

+#' Depending on data prepation, quality and desired stringency of a modification

+#' strategy, settings for cut off parameters or other variables may need to be 

+#' adjusted. This should be rarely the case, but a function for changing these

+#' settings, is implemented as the... \code{settings} function.

+#' 

+#' For changing values the input can be either a \code{list} or something 

+#' coercible to a \code{list}. Upon changing a setting, the validity of the

+#' value in terms of type(!) and dimensions will be checked. 

+#' 

+#' If settings have been modified after the data was loaded, the data is 

+#' potentially invalid. To update the data, run the \code{aggregate} or the 

+#' \code{modify} function.

+#' 

+#' @param x a \code{Modifier} or \code{ModifierSet} class

+#' @param name name of the setting to be returned or set

+#' @param value value of the setting to be set

+#' 

+#' @return 

+#' If \code{name} is omitted, \code{settings} returns a list of all settings.

+#' If \code{name} is set, \code{settings} returns a single settings or 

+#' \code{NULL}, if a value for \code{name} is not available. 

+#' 

+#' @examples 

+#' data(msi,package="RNAmodR")

+#' mi <- msi[[1]]

+#' # returns a list of all settings

+#' settings(mi)

+#' # accesses a specific setting

+#' settings(mi,"minCoverage")

+#' # modification of setting

+#' settings(mi) <- list(minCoverage = 11L)

+NULL

+

+#' @rdname settings

+#' @export

 setMethod(f = "settings",

           signature = signature(x = "Modifier"),

           definition = function(x, name){

@@ -523,36 +596,24 @@ setMethod(f = "settings",

             x@arguments[[name]]

           }

 )

-#' @rdname Modifier-functions

-#' @export

-setReplaceMethod(f = "settings",

-          signature = signature(x = "Modifier"),

-          definition = function(x, value){

-            if(is.null(names(value)) && length(value) > 0L){

-              stop("'value' has to be a named.")

-            }

-            if(!is.list(value)){

-              value <- as.list(value)

-            }

-            value <- .norm_args(value)

-            x@arguments[names(value)] <- unname(value)

-            x@aggregateValidForCurrentArguments <- FALSE

-            x@modificationsValidForCurrentArguments <- FALSE

-            x

-          })

-#' @rdname Modifier-functions

-#' @export

-setMethod(f = "validAggregate",

-          signature = signature(x = "Modifier"),

-          definition = function(x) x@aggregateValidForCurrentArguments

-)

-#' @rdname Modifier-functions

+#' @rdname settings

 #' @export

-setMethod(f = "validModification",

-          signature = signature(x = "Modifier"),

-          definition = function(x) x@modificationsValidForCurrentArguments

-)

+setReplaceMethod(f = "settings",

+                 signature = signature(x = "Modifier"),

+                 definition = function(x, value){

+                   if(is.null(names(value)) && length(value) > 0L){

+                     stop("'value' has to be a named.")

+                   }

+                   if(!is.list(value)){

+                     value <- as.list(value)

+                   }

+                   value <- .norm_args(value)

+                   x@arguments[names(value)] <- unname(value)

+                   x@aggregateValidForCurrentArguments <- FALSE

+                   x@modificationsValidForCurrentArguments <- FALSE

+                   x

+                 })

 # constructors -----------------------------------------------------------------

@@ -560,7 +621,7 @@ setMethod(f = "validModification",

   if(is(ans,"character") && extends(ans,"Modifier")){

     ans <- getClass(ans)@prototype

   } else if(!is(ans,"Modifier")) {

-    stop("Something went wrong.")

+    stop("")

   }

   .check_Modifier_data_elements(ans, list)

   if(length(list) == 1L){

@@ -604,7 +665,8 @@ setMethod(f = "validModification",

       bamfiles <- bamfiles[match(class,names(bamfiles))]

       data <- BiocParallel::bpmapply(.load_SequenceData, classes, bamfiles,

                                      MoreArgs = list(annotation, sequences,

-                                                     seqinfo, args))

+                                                     seqinfo, args),

+                                     SIMPLIFY = FALSE)

     } else {

       data <- BiocParallel::bplapply(classes, .load_SequenceData, bamfiles,

                                      annotation, sequences, seqinfo, args)

@@ -621,7 +683,7 @@ setMethod(f = "validModification",

                    })

     data <- as(data,"SequenceDataSet")

   } else {

-    stop("Something went wrong.")

+    stop("")

   }

   data

 }

@@ -678,7 +740,7 @@ setMethod(f = "validModification",

 #' @export

 setGeneric(

   name = "Modifier",

-  signature = c("x"),

+  signature = "x",

   def = function(className, x, annotation, sequences, seqinfo, ...)

     standardGeneric("Modifier")

 )

@@ -842,9 +904,6 @@ setMethod(f = "aggregate",

           signature = signature(x = "Modifier"),

           definition =

             function(x, force = FALSE){

-              if(missing(force)){

-                force <- FALSE

-              }

               assertive::assert_is_a_bool(force)

               if(!hasAggregateData(x) || force){

                 x@aggregate <- .check_aggregate_modifier(aggregateData(x), x)

@@ -935,9 +994,6 @@ setMethod(f = "modify",

           signature = signature(x = "Modifier"),

           definition =

             function(x, force = FALSE){

-              if(missing(force)){

-                force <- FALSE

-              }

               assertive::assert_is_a_bool(force)

               if(!validAggregate(x) | force){

                 x <- aggregate(x, force = TRUE)

@@ -62,9 +62,6 @@ NULL

 NULL

 .norm_prediction_args <- function(input){

-  if(missing(input)){

-    input <- list()

-  }

   if(!is.list(input)){

     stop("'prediction.args' must be a list.")

   }

@@ -79,9 +76,6 @@ NULL

 .rocr_exclusive_functions <- c("rch","auc","prbe","mxe","rmse","ecost")

 .norm_performance_args <- function(input, x){

-  if(missing(input)){

-    input <- list()

-  }

   if(!is.list(input)){

     stop("'performance.args' must be a list.")

   }

@@ -102,11 +96,8 @@ NULL

     }

   }

   if(!is.null(input[["x.measure"]])){

-    if(length(input[["x.measure"]]) == 0L){

-      x.measure <- "cutoff"

-    } else if(is.na(input[["x.measure"]])){

-      x.measure <- "cutoff"

-    } else if(input[["x.measure"]] == ""){

+    if(length(input[["x.measure"]]) == 0L || is.na(input[["x.measure"]]) || 

+       input[["x.measure"]] == ""){

       x.measure <- "cutoff"

     } else {

       x.measure <- input[["x.measure"]]

@@ -136,9 +127,6 @@ NULL

 }

 .norm_plot_args <- function(input){

-  if(missing(input)){

-    input <- list()

-  }

   if(!is.list(input)){

     stop("'plot.args' must be a list.")

   }

@@ -232,9 +220,9 @@ NULL

   colnames <- colnames[colnames != "labels"]

   data <- lapply(seq_along(colnames),

                  function(i){

-                   c <- colnames[i]

-                   c <- c("labels",c)

-                   d <- data[,c]

+                   cn <- colnames[i]

+                   cn <- c("labels",cn)

+                   d <- data[,cn]

                    colnames(d) <- c("labels","predictions")

                    d <- unlist(d)

                    rownames(d) <- NULL

@@ -246,8 +234,8 @@ NULL

 .get_prediction_data_ModifierSet <- function(x, coord, score){

   data <- lapply(x, .get_prediction_data_Modifier, coord, score)

-  names <- names(data[[1]])

-  data <- lapply(names,

+  data_names <- names(data[[1]])

+  data <- lapply(data_names,

                  function(name){

                    lapply(data,"[[",name)

                  })

@@ -260,7 +248,7 @@ NULL

                    list(predictions = predictions,

                         labels = labels)

                  })

-  names(data) <- names

+  names(data) <- data_names

   data

 }

@@ -289,7 +277,7 @@ NULL

     plot.args[["add"]] <- FALSE

   }

   #

-  mapply(

+  Map(

     function(d, name, colour, prediction.args, performance.args, plot.args){

       pred <- do.call(ROCR::prediction, c(list(predictions = d$predictions, 

                                                labels = d$labels), 

@@ -301,10 +289,10 @@ NULL

         stop("Error during plotting of performance object: ",tmp)

       }

       graphics::title(main = name)

-      if(plot.args[["abline"]] == TRUE){

+      if(plot.args[["abline"]]){

         graphics::abline(a = 0, b = 1)

       }

-      if(plot.args[["AUC"]] == TRUE){

+      if(plot.args[["AUC"]]){

         auc <- unlist(slot(performance(pred,"auc"),"y.values"))

         auc <- paste(c("AUC = "), round(auc,2L), sep = "")

         graphics::legend(0.55, 0.25, auc, bty = "n", cex = 1)

@@ -314,8 +302,7 @@ NULL

     names(data),

     MoreArgs = list(prediction.args = prediction.args,

                     performance.args = performance.args,

-                    plot.args = plot.args),

-    SIMPLIFY = FALSE)

+                    plot.args = plot.args))

   for(i in seq_len(n_remaining)){

     graphics::plot.new()

   }

@@ -328,11 +315,8 @@ NULL

 setMethod(

   f = "plotROC", 

   signature = signature(x = "Modifier"),

-  definition = function(x, coord, score = NULL, prediction.args, 

-                        performance.args, plot.args){

-    if(missing(score)){

-      score <- NULL

-    }

+  definition = function(x, coord, score = NULL, prediction.args = list(), 

+                        performance.args = list(), plot.args = list()){

     coord <- .norm_coord(coord, modType(x))

     data <- .get_prediction_data_Modifier(x, coord, score)

     .plot_ROCR(data,

@@ -348,11 +332,8 @@ setMethod(

 setMethod(

   f = "plotROC", 

   signature = signature(x = "ModifierSet"),

-  definition = function(x, coord, score = NULL, prediction.args,

-                        performance.args, plot.args){

-    if(missing(score)){

-      score <- NULL

-    }

+  definition = function(x, coord, score = NULL, prediction.args = list(), 

+                        performance.args = list(), plot.args = list()){

     coord <- .norm_coord(coord, modType(x))

     data <- .get_prediction_data_ModifierSet(x, coord, score)

     .plot_ROCR(data,

@@ -98,10 +98,10 @@ NULL

     lapply(x,

            function(z){

              data <- getAggregateData(z)

-             names <- .get_element_names(data, coord, args[["name"]],

+             element_names <- .get_element_names(data, coord, args[["name"]],

                                          args[["type"]])

-             data <- data[match(names, names(data))]

-             coord <- coord[match(names, names(coord))]

+             data <- data[match(element_names, names(data))]

+             coord <- coord[match(element_names, names(coord))]

              .perform_subset(data, coord, args[["flanking"]], 

                              args[["perTranscript"]])

            })

@@ -67,12 +67,12 @@ setMethod(f = "constructModRanges",

             if(any(length(positions) != data_length)){

               stop("Number of positions and scores do not match.")

             }

-            seqnames <- .get_unique_seqnames(range)

+            seqnames_unique <- .get_unique_seqnames(range)

             ranges <- IRanges::IRanges(start = positions,

                                        width = 1L)

             strand <- .get_unique_strand(range)

             mranges <- 

-              GenomicRanges::GRanges(seqnames = seqnames,

+              GenomicRanges::GRanges(seqnames = seqnames_unique,

                                      ranges = ranges,

                                      strand = strand,

                                      seqinfo = GenomeInfoDb::seqinfo(range),

@@ -2,15 +2,15 @@

 #' @include Modifier-class.R

 NULL

-#' @name visualizeData

-#' @aliases visualizeData visualizeDataByCoord getDataTrack

+#' @name plotData

+#' @aliases plotData plotDataByCoord getDataTrack

 #' 

 #' @title Visualizing data data from a \code{SequenceData}, 

 #' \code{SequenceDataSet}, \code{SequenceDataList}, \code{Modifier} or 

 #' \code{ModifierSet} object.

 #' 

 #' @description 

-#' With the \code{visualizeData} and \code{visualizeDataByCoord} functions data

+#' With the \code{plotData} and \code{plotDataByCoord} functions data

 #' from a \code{SequenceData}, \code{SequenceDataSet}, \code{SequenceDataList},

 #' \code{Modifier} or \code{ModifierSet} object can be visualized.

 #' 

@@ -27,9 +27,9 @@ NULL

 #' @param coord coordinates of a positions to subset to as a 

 #' \code{GRanges} object. The 'Parent' column is expected to match the 

 #' transcript name.

-#' @param name Only for \code{visualizeData}: the transcript name

-#' @param from Only for \code{visualizeData}: start position

-#' @param to Only for \code{visualizeData}: end position

+#' @param name Only for \code{plotData}: the transcript name

+#' @param from Only for \code{plotData}: start position

+#' @param to Only for \code{plotData}: end position

 #' @param type the data type of data show as data tracks.

 #' @param showSequenceData \code{TRUE} or \code{FALSE}: should the sequence data

 #' be shown? (default: \code{seqdata = FALSE})

@@ -60,14 +60,14 @@ NULL

 #' 

 #' @examples 

 #' data(msi,package="RNAmodR")

-#' visualizeData(msi[[1]], "2", from = 10L, to = 45L)

+#' plotData(msi[[1]], "2", from = 10L, to = 45L)

 #' \dontrun{

-#' visualizeData(msi, "2", from = 10L, to = 45L)

+#' plotData(msi, "2", from = 10L, to = 45L)

 #' }

 NULL

 .norm_show_argument <- function(show_arg, default = FALSE){

-  if(missing(show_arg) || !assertive::is_a_bool(show_arg)){

+  if(!assertive::is_a_bool(show_arg)){

     show_arg <- default

   }

   show_arg

@@ -143,23 +143,23 @@ NULL

 # ------------------------------------------------------------------------------

-#' @rdname visualizeData

+#' @rdname plotData

 setMethod(

-  f = "visualizeDataByCoord",

+  f = "plotDataByCoord",

   signature = signature(x = "Modifier", coord = "GRanges"),

   definition = function(x, coord, type = NA, window.size = 15L, ...) {

     # input check

     coord <- .norm_coord_for_visualization(ranges(x), coord)

     from_to <- .get_viz_from_to_coord(ranges(x), coord, window.size)

-    visualizeData(x, name = coord$Parent, from = from_to$from,

+    plotData(x, name = coord$Parent, from = from_to$from,

                   to = from_to$to, type = type, ...)

   }