Browse code

refactored code based upon review

Felix Ernst authored on 23/05/2019 08:51:38
Showing47 changed files

... ...
@@ -38,6 +38,8 @@ export(modify)
38 38
 export(pileupToCoverage)
39 39
 export(plotCompare)
40 40
 export(plotCompareByCoord)
41
+export(plotData)
42
+export(plotDataByCoord)
41 43
 export(plotROC)
42 44
 export(replicates)
43 45
 export(sequenceData)
... ...
@@ -46,8 +48,6 @@ export(settings)
46 48
 export(subsetByCoord)
47 49
 export(validAggregate)
48 50
 export(validModification)
49
-export(visualizeData)
50
-export(visualizeDataByCoord)
51 51
 exportClasses(CoverageSequenceData)
52 52
 exportClasses(End3SequenceData)
53 53
 exportClasses(End5SequenceData)
... ...
@@ -89,6 +89,8 @@ exportMethods(modify)
89 89
 exportMethods(names)
90 90
 exportMethods(pileupToCoverage)
91 91
 exportMethods(plotCompareByCoord)
92
+exportMethods(plotData)
93
+exportMethods(plotDataByCoord)
92 94
 exportMethods(plotROC)
93 95
 exportMethods(ranges)
94 96
 exportMethods(replicates)
... ...
@@ -99,8 +101,6 @@ exportMethods(settings)
99 101
 exportMethods(subsetByCoord)
100 102
 exportMethods(validAggregate)
101 103
 exportMethods(validModification)
102
-exportMethods(visualizeData)
103
-exportMethods(visualizeDataByCoord)
104 104
 import(GenomicRanges)
105 105
 import(Gviz)
106 106
 import(S4Vectors)
... ...
@@ -16,7 +16,7 @@ NULL
16 16
 #' @export
17 17
 setGeneric( 
18 18
   name = "plotROC",
19
-  signature = c("x"),
19
+  signature = "x",
20 20
   def = function(x, coord, ...)
21 21
     standardGeneric("plotROC")
22 22
 )
... ...
@@ -81,35 +81,35 @@ setGeneric(
81 81
 #' @rdname Modifier-functions
82 82
 #' @export
83 83
 setGeneric( 
84
-  name = "settings",
85
-  def = function(x, name = NULL) standardGeneric("settings")
84
+  name = "validAggregate",
85
+  def = function(x) standardGeneric("validAggregate")
86 86
 )
87 87
 #' @rdname Modifier-functions
88 88
 #' @export
89 89
 setGeneric( 
90
-  name = "settings<-",
91
-  def = function(x, name, value) standardGeneric("settings<-")
90
+  name = "validModification",
91
+  def = function(x) standardGeneric("validModification")
92 92
 )
93
-#' @rdname Modifier-functions
93
+
94
+#' @rdname settings
94 95
 #' @export
95 96
 setGeneric( 
96
-  name = "validAggregate",
97
-  def = function(x) standardGeneric("validAggregate")
97
+  name = "settings",
98
+  def = function(x, name = NULL) standardGeneric("settings")
98 99
 )
99
-#' @rdname Modifier-functions
100
+#' @rdname settings
100 101
 #' @export
101 102
 setGeneric( 
102
-  name = "validModification",
103
-  def = function(x) standardGeneric("validModification")
103
+  name = "settings<-",
104
+  def = function(x, name, value) standardGeneric("settings<-")
104 105
 )
105
-
106 106
 # Modifier/ModifierSet functions -----------------------------------------------
107 107
 
108 108
 #' @rdname modify
109 109
 #' @export
110 110
 setGeneric( 
111 111
   name = "modify",
112
-  signature = c("x"),
112
+  signature = "x",
113 113
   def = function(x, ...) standardGeneric("modify")
114 114
 )
115 115
 
... ...
@@ -117,7 +117,7 @@ setGeneric(
117 117
 #' @export
118 118
 setGeneric( 
119 119
   name = "findMod",
120
-  signature = c("x"),
120
+  signature = "x",
121 121
   def = function(x) standardGeneric("findMod")
122 122
 )
123 123
 
... ...
@@ -128,7 +128,7 @@ setGeneric(
128 128
 #' @export
129 129
 setGeneric( 
130 130
   name = "aggregate",
131
-  signature = c("x"),
131
+  signature = "x",
132 132
   def = function(x, ...) standardGeneric("aggregate")
133 133
 )
134 134
 #' @rdname aggregate
... ...
@@ -141,14 +141,14 @@ setGeneric(
141 141
 #' @export
142 142
 setGeneric( 
143 143
   name = "getAggregateData",
144
-  signature = c("x"),
144
+  signature = "x",
145 145
   def = function(x) standardGeneric("getAggregateData")
146 146
 )
147 147
 #' @rdname aggregate
148 148
 #' @export
149 149
 setGeneric( 
150 150
   name = "hasAggregateData",
151
-  signature = c("x"),
151
+  signature = "x",
152 152
   def = function(x) standardGeneric("hasAggregateData")
153 153
 ) 
154 154
 
... ...
@@ -170,27 +170,27 @@ setGeneric(
170 170
   def = function(x, coord, ...)
171 171
     standardGeneric("labelByCoord")
172 172
 )
173
-#' @rdname visualizeData
173
+#' @rdname plotData
174 174
 #' @export
175 175
 setGeneric(
176
-  name = "visualizeData",
177
-  signature = c("x"),
176
+  name = "plotData",
177
+  signature = "x",
178 178
   def = function(x, name, from = 1L, to = 30L, type, ...)
179
-    standardGeneric("visualizeData")
179
+    standardGeneric("plotData")
180 180
 )
181
-#' @rdname visualizeData
181
+#' @rdname plotData
182 182
 #' @export
183 183
 setGeneric(
184
-  name = "visualizeDataByCoord",
184
+  name = "plotDataByCoord",
185 185
   signature = c("x","coord"),
186 186
   def = function(x, coord, type, window.size = 15L, ...)
187
-    standardGeneric("visualizeDataByCoord")
187
+    standardGeneric("plotDataByCoord")
188 188
 )
189
-#' @rdname visualizeData
189
+#' @rdname plotData
190 190
 #' @export
191 191
 setGeneric(
192 192
   name = "getDataTrack",
193
-  signature = c("x"),
193
+  signature = "x",
194 194
   def = function(x, name, ...)
195 195
     standardGeneric("getDataTrack")
196 196
 )
... ...
@@ -201,7 +201,7 @@ setGeneric(
201 201
 #' @export
202 202
 setGeneric( 
203 203
   name = "compare",
204
-  signature = c("x"),
204
+  signature = "x",
205 205
   def = function(x, name, from = 1L, to = 30L, ...)
206 206
     standardGeneric("compare")
207 207
 ) 
... ...
@@ -217,7 +217,7 @@ setGeneric(
217 217
 #' @export
218 218
 setGeneric( 
219 219
   name = "plotCompare",
220
-  signature = c("x"),
220
+  signature = "x",
221 221
   def = function(x, name, from = 1L, to = 30L, normalize, ...)
222 222
     standardGeneric("plotCompare")
223 223
 ) 
... ...
@@ -105,10 +105,10 @@ NULL
105 105
 #' see also the man pages for the functions mentioned below.
106 106
 #' @param value See \code{\link[RNAmodR:Modifier-functions]{settings}}
107 107
 #' @param coord,name,from,to,type,window.size,... See 
108
-#' \code{\link{visualizeData}}
108
+#' \code{\link{plotData}}
109 109
 #' 
110 110
 #' @details 
111
-#' \code{ModInosine} specific arguments for \link{visualizeData}:
111
+#' \code{ModInosine} specific arguments for \link{plotData}:
112 112
 #' \itemize{
113 113
 #' \item{\code{colour.bases} - }{a named character vector of \code{length = 4} 
114 114
 #' for the colours of the individual bases. The names are expected to be 
... ...
@@ -122,9 +122,9 @@ NULL
122 122
 #' \item{\code{modify}} {See \code{\link{modify}}.}
123 123
 #' \item{\code{getDataTrack}} {a list of 
124 124
 #' \code{\link[Gviz:DataTrack-class]{DataTrack}} objects. See 
125
-#' \code{\link{visualizeDataByCoord}}.}
126
-#' \item{\code{visualizeData}} {See \code{\link{visualizeDataByCoord}}.}
127
-#' \item{\code{visualizeDataByCoord}} {See \code{\link{visualizeDataByCoord}}.}
125
+#' \code{\link{plotDataByCoord}}.}
126
+#' \item{\code{plotData}} {See \code{\link{plotDataByCoord}}.}
127
+#' \item{\code{plotDataByCoord}} {See \code{\link{plotDataByCoord}}.}
128 128
 #' }
129 129
 #' 
130 130
 #' @examples 
... ...
@@ -227,7 +227,7 @@ setMethod(f = "aggregateData",
227 227
 
228 228
 .find_inosine <- function(x){
229 229
   if(!hasAggregateData(x)){
230
-    stop("Something went wrong.")
230
+    stop("")
231 231
   }
232 232
   letters <- IRanges::CharacterList(strsplit(as.character(sequences(x)),""))
233 233
   # get the aggregate data
... ...
@@ -243,7 +243,7 @@ setMethod(f = "aggregateData",
243 243
   # find inosine positions by looking for A to G conversion at position with 
244 244
   # enough coverage
245 245
   grl <- ranges(x)
246
-  modifications <- mapply(
246
+  modifications <- Map(
247 247
     function(m,c,l,r){
248 248
       m <- m[l == "A" &
249 249
                m$score >= minScore & 
... ...
@@ -257,19 +257,17 @@ setMethod(f = "aggregateData",
257 257
     mod,
258 258
     coverage,
259 259
     letters,
260
-    grl,
261
-    SIMPLIFY = FALSE)
260
+    grl)
262 261
   f <- !vapply(modifications,
263 262
                is.null,
264 263
                logical(1))
265
-  modifications <- mapply(
264
+  modifications <- Map(
266 265
     function(m,name){
267 266
       m$Parent <- name
268 267
       m
269 268
     },
270 269
     modifications[f],
271
-    names(grl)[f],
272
-    SIMPLIFY = FALSE)
270
+    names(grl)[f])
273 271
   modifications <- GenomicRanges::GRangesList(modifications)
274 272
   unname(unlist(modifications))
275 273
 }
... ...
@@ -2,10 +2,10 @@
2 2
 #' @include Modifier-Inosine-class.R
3 3
 NULL
4 4
 
5
-RNAMODR_I_PLOT_DATA <- c("score")
6
-RNAMODR_I_PLOT_DATA_DEFAULT <- c("score")
5
+RNAMODR_I_PLOT_DATA <- "score"
6
+RNAMODR_I_PLOT_DATA_DEFAULT <- "score"
7 7
 
8
-RNAMODR_I_PLOT_DATA_COLOURS <- c("score" = "#ABABAB") 
8
+RNAMODR_I_PLOT_DATA_COLOURS <- c(score = "#ABABAB") 
9 9
 RNAMODR_I_PLOT_DATA_NAMES <- c(score = "Score Inosine")
10 10
 
11 11
 .norm_viz_mod_inosine_args <- function(input, type){
... ...
@@ -66,7 +66,7 @@ setMethod(
66 66
 #' @rdname ModInosine-functions
67 67
 #' @export
68 68
 setMethod(
69
-  f = "visualizeDataByCoord",
69
+  f = "plotDataByCoord",
70 70
   signature = signature(x = "ModInosine", coord = "GRanges"),
71 71
   definition = function(x, coord, type = "score", window.size = 15L, ...) {
72 72
     if(missing(type)){
... ...
@@ -80,7 +80,7 @@ setMethod(
80 80
 #' @rdname ModInosine-functions
81 81
 #' @export
82 82
 setMethod(
83
-  f = "visualizeData",
83
+  f = "plotData",
84 84
   signature = signature(x = "ModInosine"),
85 85
   definition = function(x, name, from, to, type = "score", ...) {
86 86
     if(missing(type)){
... ...
@@ -94,7 +94,7 @@ setMethod(
94 94
 #' @rdname ModInosine-functions
95 95
 #' @export
96 96
 setMethod(
97
-  f = "visualizeDataByCoord",
97
+  f = "plotDataByCoord",
98 98
   signature = signature(x = "ModSetInosine", coord = "GRanges"),
99 99
   definition = function(x, coord, type = "score", window.size = 15L, ...) {
100 100
     if(missing(type)){
... ...
@@ -108,7 +108,7 @@ setMethod(
108 108
 #' @rdname ModInosine-functions
109 109
 #' @export
110 110
 setMethod(
111
-  f = "visualizeData",
111
+  f = "plotData",
112 112
   signature = signature(x = "ModSetInosine"),
113 113
   definition = function(x, name, from, to, type = "score", ...) {
114 114
     if(missing(type)){
... ...
@@ -5,6 +5,10 @@
5 5
 #' @include Modifier-utils.R
6 6
 NULL
7 7
 
8
+invalidMessage <- paste0("Settings were changed after data aggregation or ",
9
+                         "modification search. Rerun with modify(x,force = ",
10
+                         "TRUE) to update with current settings.")
11
+
8 12
 #' @name Modifier-class
9 13
 #' @aliases Modifier
10 14
 #'
... ...
@@ -61,6 +65,11 @@ NULL
61 65
 #' For this example a \code{list} of \code{character} vectors is expected.
62 66
 #' Each element must be named according to the names of \code{dataType()} and
63 67
 #' contain a \code{character} vector for creating a \code{SequenceData} object.
68
+#' 
69
+#' All additional options must be named and will be passed to the
70
+#' \code{\link[=settings]{settings}} function and onto the \code{SequenceData}
71
+#' objects, if \code{x} is not a \code{SequenceData} object or a list of
72
+#' \code{SequenceData} objects.
64 73
 #'
65 74
 #' @param className The name of the class which should be constructed.
66 75
 #' @param x the input which can be of the following types
... ...
@@ -89,10 +98,12 @@ NULL
89 98
 #' \item{\code{find.mod}:} {\code{TRUE} or \code{FALSE}: should the search for
90 99
 #' for modifications be triggered upon construction? If not the search can be
91 100
 #' started by calling the \code{modify()} function.}
101
+#' \item{additional parameters depending on the specific \code{Modifier} class}
92 102
 #' }
93
-#' All other arguments will be passed onto the \code{SequenceData} objects, if
94
-#' \code{x} is not a \code{SequenceData} object or a list of \code{SequenceData}
95
-#' objects.
103
+#' All additional options must be named and will be passed to the
104
+#' \code{\link[=settings]{settings}} function and onto the \code{SequenceData}
105
+#' objects, if \code{x} is not a \code{SequenceData} object or a list of
106
+#' \code{SequenceData} objects.
96 107
 #'
97 108
 #' @slot mod a \code{character} value, which needs to contain one or more
98 109
 #' elements from the alphabet of a
... ...
@@ -125,10 +136,13 @@ NULL
125 136
 #' @description
126 137
 #' For the \code{Modifier} and  \code{ModifierSet} classes a number of functions
127 138
 #' are implemented to access the data stored by the object.
139
+#' 
140
+#' The \code{validAggregate} and \code{validModification} functions check if
141
+#' \code{\link[=settings]{settings}} have been modified, after the data was 
142
+#' loaded. This potentially invalidates them. To update the data, run the
143
+#' \code{aggregate} or the \code{modify} function.
128 144
 #'
129 145
 #' @param x,object a \code{Modifier} or \code{ModifierSet} class
130
-#' @param name For \code{settings}: name of the setting to be returned or set
131
-#' @param value For \code{settings}: value of the setting to be set
132 146
 #' @param modified For \code{sequences}: \code{TRUE} or \code{FALSE}: Should
133 147
 #' the sequences be returned as a \code{ModRNAString} with the found
134 148
 #' modifications added on top of the \code{RNAString}? See
... ...
@@ -142,7 +156,6 @@ NULL
142 156
 #' \item{\code{modifierType}:} {a character vector with the appropriate class
143 157
 #' Name of a \code{\link[=Modifier-class]{Modifier}}.}
144 158
 #' \item{\code{mainScore}:} {a character vector.}
145
-#' \item{\code{settings}:} {a \code{Seqinfo} object.}
146 159
 #' \item{\code{sequenceData}:} {a \code{SequenceData} object.}
147 160
 #' \item{\code{modifications}:} {a \code{GRanges} or \code{GRangesList} object
148 161
 #' describing the found modifications.}
... ...
@@ -151,7 +164,13 @@ NULL
151 164
 #' \item{\code{ranges}:} {a \code{GRangesList} object with each element per
152 165
 #' transcript.}
153 166
 #' \item{\code{bamfiles}:} {a \code{BamFileList} object.}
167
+#' \item{\code{validAggregate}:} {\code{TRUE} or \code{FALSE}. Checks if current
168
+#' settings are the same for which the data was aggregate}
169
+#' \item{\code{validModification}:} {\code{TRUE} or \code{FALSE}. Checks if 
170
+#' current settings are the same for which modification were found}
154 171
 #' }
172
+#' 
173
+#' @seealso \code{\link[=settings]{settings}}
155 174
 #'
156 175
 #' @examples
157 176
 #' data(msi,package="RNAmodR")
... ...
@@ -159,7 +178,6 @@ NULL
159 178
 #' modifierType(mi) # The class name of the Modifier object
160 179
 #' modifierType(msi) #
161 180
 #' mainScore(mi)
162
-#' settings(mi)
163 181
 #' sequenceData(mi)
164 182
 #' modifications(mi)
165 183
 #' # general accessors
... ...
@@ -196,18 +214,18 @@ setClass("Modifier",
196 214
 
197 215
 # validity ---------------------------------------------------------------------
198 216
 
199
-.check_SequenceData_elements <- function(x, list){
200
-  if(is(list,"SequenceData")){
201
-    list <- list(list)
202
-  } else if(is(list,"list")){
203
-    elementTypeMatch <- !vapply(list,is,logical(1),"SequenceData")
217
+.check_SequenceData_elements <- function(x, data){
218
+  if(is(data,"SequenceData")){
219
+    data <- list(data)
220
+  } else if(is(data,"list")){
221
+    elementTypeMatch <- !vapply(data,is,logical(1),"SequenceData")
204 222
     if(any(elementTypeMatch)){
205 223
       stop("Not all elements are 'SequenceData' objects.", call. = FALSE)
206 224
     }
207
-  } else if(!is(list,"SequenceDataSet")){
208
-   stop("Something went wrong.")
225
+  } else if(!is(data,"SequenceDataSet")){
226
+    stop("")
209 227
   }
210
-  elementTypes <- vapply(list,class,character(1))
228
+  elementTypes <- vapply(data,class,character(1))
211 229
   if(length(elementTypes) != length(dataType(x))){
212 230
     stop("Number of 'SequenceData' elements does not match the requirements of",
213 231
          " ",class(x),". '",paste(dataType(x), collapse = "','"),"' are ",
... ...
@@ -222,8 +240,8 @@ setClass("Modifier",
222 240
   NULL
223 241
 }
224 242
 
225
-.check_SequenceDataList_data_elements <- function(x, list){
226
-  ans <- lapply(list, .check_SequenceData_elements, x)
243
+.check_SequenceDataList_data_elements <- function(x, data){
244
+  ans <- lapply(data, .check_SequenceData_elements, x)
227 245
   if(all(vapply(ans,is.null))) {
228 246
     return(NULL)
229 247
   }
... ...
@@ -296,9 +314,9 @@ S4Vectors::setValidity2(Class = "Modifier", .valid_Modifier)
296 314
                        settings[,f,drop = FALSE]
297 315
                      })
298 316
   if(is.null(rownames(settings[[1]]))){
299
-    names <- rep(" ",nrow(settings[[1]]))
317
+    setting_names <- rep(" ",nrow(settings[[1]]))
300 318
   } else {
301
-    names <- rownames(settings[[1]])
319
+    setting_names <- rownames(settings[[1]])
302 320
   }
303 321
   for(i in seq_along(settings)){
304 322
     out <-
... ...
@@ -312,7 +330,7 @@ S4Vectors::setValidity2(Class = "Modifier", .valid_Modifier)
312 330
       }), use.names = FALSE), nrow = 1,
313 331
       dimnames = list("", colnames(out)))
314 332
     out <- rbind(classinfo, out)
315
-    rownames(out) <- c(" ",names)
333
+    rownames(out) <- c(" ",setting_names)
316 334
     print(out, quote = FALSE, right = TRUE)
317 335
   }
318 336
 }
... ...
@@ -347,9 +365,7 @@ setMethod(
347 365
     .show_settings(settings)
348 366
     valid <- c(validAggregate(object), validModification(object))
349 367
     if(!all(valid)){
350
-      warning("Settings were changed after data aggregation or modification ",
351
-              "search. Rerun with modify(x,force = TRUE) to update with ",
352
-              "current settings.", call. = FALSE)
368
+      warning(invalidMessage, call. = FALSE)
353 369
     }
354 370
   }
355 371
 )
... ...
@@ -404,6 +420,10 @@ setMethod(f = "modifications",
404 420
               if(!assertive::is_a_bool(perTranscript)){
405 421
                 stop("'perTranscript' has to be a single logical value.")
406 422
               }
423
+              valid <- c(validAggregate(x), validModification(x))
424
+              if(!all(valid)){
425
+                warning(invalidMessage, call. = FALSE)
426
+              }
407 427
               if(perTranscript){
408 428
                 return(.get_modifications_per_transcript(x))
409 429
               }
... ...
@@ -457,7 +477,7 @@ setMethod(f = "sequences",
457 477
                 stop("'modified' has to be a single logical value.",
458 478
                      call. = FALSE)
459 479
               }
460
-              if(modified == FALSE){
480
+              if(!modified){
461 481
                 return(sequences(sequenceData(x)))
462 482
               }
463 483
               mod <- .get_modifications_per_transcript(x)
... ...
@@ -511,6 +531,59 @@ setMethod(f = "seqinfo",
511 531
 
512 532
 #' @rdname Modifier-functions
513 533
 #' @export
534
+setMethod(f = "validAggregate",
535
+          signature = signature(x = "Modifier"),
536
+          definition = function(x) x@aggregateValidForCurrentArguments
537
+)
538
+#' @rdname Modifier-functions
539
+#' @export
540
+setMethod(f = "validModification",
541
+          signature = signature(x = "Modifier"),
542
+          definition = function(x) x@modificationsValidForCurrentArguments
543
+)
544
+
545
+# settings ---------------------------------------------------------------------
546
+
547
+#' @name settings
548
+#' 
549
+#' @title Settings for \code{Modifier} objects
550
+#' 
551
+#' @description 
552
+#' Depending on data prepation, quality and desired stringency of a modification
553
+#' strategy, settings for cut off parameters or other variables may need to be 
554
+#' adjusted. This should be rarely the case, but a function for changing these
555
+#' settings, is implemented as the... \code{settings} function.
556
+#' 
557
+#' For changing values the input can be either a \code{list} or something 
558
+#' coercible to a \code{list}. Upon changing a setting, the validity of the
559
+#' value in terms of type(!) and dimensions will be checked. 
560
+#' 
561
+#' If settings have been modified after the data was loaded, the data is 
562
+#' potentially invalid. To update the data, run the \code{aggregate} or the 
563
+#' \code{modify} function.
564
+#' 
565
+#' @param x a \code{Modifier} or \code{ModifierSet} class
566
+#' @param name name of the setting to be returned or set
567
+#' @param value value of the setting to be set
568
+#' 
569
+#' @return 
570
+#' If \code{name} is omitted, \code{settings} returns a list of all settings.
571
+#' If \code{name} is set, \code{settings} returns a single settings or 
572
+#' \code{NULL}, if a value for \code{name} is not available. 
573
+#' 
574
+#' @examples 
575
+#' data(msi,package="RNAmodR")
576
+#' mi <- msi[[1]]
577
+#' # returns a list of all settings
578
+#' settings(mi)
579
+#' # accesses a specific setting
580
+#' settings(mi,"minCoverage")
581
+#' # modification of setting
582
+#' settings(mi) <- list(minCoverage = 11L)
583
+NULL
584
+
585
+#' @rdname settings
586
+#' @export
514 587
 setMethod(f = "settings",
515 588
           signature = signature(x = "Modifier"),
516 589
           definition = function(x, name){
... ...
@@ -523,36 +596,24 @@ setMethod(f = "settings",
523 596
             x@arguments[[name]]
524 597
           }
525 598
 )
526
-#' @rdname Modifier-functions
527
-#' @export
528
-setReplaceMethod(f = "settings",
529
-          signature = signature(x = "Modifier"),
530
-          definition = function(x, value){
531
-            if(is.null(names(value)) && length(value) > 0L){
532
-              stop("'value' has to be a named.")
533
-            }
534
-            if(!is.list(value)){
535
-              value <- as.list(value)
536
-            }
537
-            value <- .norm_args(value)
538
-            x@arguments[names(value)] <- unname(value)
539
-            x@aggregateValidForCurrentArguments <- FALSE
540
-            x@modificationsValidForCurrentArguments <- FALSE
541
-            x
542
-          })
543 599
 
544
-#' @rdname Modifier-functions
545
-#' @export
546
-setMethod(f = "validAggregate",
547
-          signature = signature(x = "Modifier"),
548
-          definition = function(x) x@aggregateValidForCurrentArguments
549
-)
550
-#' @rdname Modifier-functions
600
+#' @rdname settings
551 601
 #' @export
552
-setMethod(f = "validModification",
553
-          signature = signature(x = "Modifier"),
554
-          definition = function(x) x@modificationsValidForCurrentArguments
555
-)
602
+setReplaceMethod(f = "settings",
603
+                 signature = signature(x = "Modifier"),
604
+                 definition = function(x, value){
605
+                   if(is.null(names(value)) && length(value) > 0L){
606
+                     stop("'value' has to be a named.")
607
+                   }
608
+                   if(!is.list(value)){
609
+                     value <- as.list(value)
610
+                   }
611
+                   value <- .norm_args(value)
612
+                   x@arguments[names(value)] <- unname(value)
613
+                   x@aggregateValidForCurrentArguments <- FALSE
614
+                   x@modificationsValidForCurrentArguments <- FALSE
615
+                   x
616
+                 })
556 617
 
557 618
 # constructors -----------------------------------------------------------------
558 619
 
... ...
@@ -560,7 +621,7 @@ setMethod(f = "validModification",
560 621
   if(is(ans,"character") && extends(ans,"Modifier")){
561 622
     ans <- getClass(ans)@prototype
562 623
   } else if(!is(ans,"Modifier")) {
563
-    stop("Something went wrong.")
624
+    stop("")
564 625
   }
565 626
   .check_Modifier_data_elements(ans, list)
566 627
   if(length(list) == 1L){
... ...
@@ -604,7 +665,8 @@ setMethod(f = "validModification",
604 665
       bamfiles <- bamfiles[match(class,names(bamfiles))]
605 666
       data <- BiocParallel::bpmapply(.load_SequenceData, classes, bamfiles,
606 667
                                      MoreArgs = list(annotation, sequences,
607
-                                                     seqinfo, args))
668
+                                                     seqinfo, args),
669
+                                     SIMPLIFY = FALSE)
608 670
     } else {
609 671
       data <- BiocParallel::bplapply(classes, .load_SequenceData, bamfiles,
610 672
                                      annotation, sequences, seqinfo, args)
... ...
@@ -621,7 +683,7 @@ setMethod(f = "validModification",
621 683
                    })
622 684
     data <- as(data,"SequenceDataSet")
623 685
   } else {
624
-    stop("Something went wrong.")
686
+    stop("")
625 687
   }
626 688
   data
627 689
 }
... ...
@@ -678,7 +740,7 @@ setMethod(f = "validModification",
678 740
 #' @export
679 741
 setGeneric(
680 742
   name = "Modifier",
681
-  signature = c("x"),
743
+  signature = "x",
682 744
   def = function(className, x, annotation, sequences, seqinfo, ...)
683 745
     standardGeneric("Modifier")
684 746
 )
... ...
@@ -842,9 +904,6 @@ setMethod(f = "aggregate",
842 904
           signature = signature(x = "Modifier"),
843 905
           definition =
844 906
             function(x, force = FALSE){
845
-              if(missing(force)){
846
-                force <- FALSE
847
-              }
848 907
               assertive::assert_is_a_bool(force)
849 908
               if(!hasAggregateData(x) || force){
850 909
                 x@aggregate <- .check_aggregate_modifier(aggregateData(x), x)
... ...
@@ -935,9 +994,6 @@ setMethod(f = "modify",
935 994
           signature = signature(x = "Modifier"),
936 995
           definition =
937 996
             function(x, force = FALSE){
938
-              if(missing(force)){
939
-                force <- FALSE
940
-              }
941 997
               assertive::assert_is_a_bool(force)
942 998
               if(!validAggregate(x) | force){
943 999
                 x <- aggregate(x, force = TRUE)
... ...
@@ -62,9 +62,6 @@ NULL
62 62
 NULL
63 63
 
64 64
 .norm_prediction_args <- function(input){
65
-  if(missing(input)){
66
-    input <- list()
67
-  }
68 65
   if(!is.list(input)){
69 66
     stop("'prediction.args' must be a list.")
70 67
   }
... ...
@@ -79,9 +76,6 @@ NULL
79 76
 
80 77
 .rocr_exclusive_functions <- c("rch","auc","prbe","mxe","rmse","ecost")
81 78
 .norm_performance_args <- function(input, x){
82
-  if(missing(input)){
83
-    input <- list()
84
-  }
85 79
   if(!is.list(input)){
86 80
     stop("'performance.args' must be a list.")
87 81
   }
... ...
@@ -102,11 +96,8 @@ NULL
102 96
     }
103 97
   }
104 98
   if(!is.null(input[["x.measure"]])){
105
-    if(length(input[["x.measure"]]) == 0L){
106
-      x.measure <- "cutoff"
107
-    } else if(is.na(input[["x.measure"]])){
108
-      x.measure <- "cutoff"
109
-    } else if(input[["x.measure"]] == ""){
99
+    if(length(input[["x.measure"]]) == 0L || is.na(input[["x.measure"]]) || 
100
+       input[["x.measure"]] == ""){
110 101
       x.measure <- "cutoff"
111 102
     } else {
112 103
       x.measure <- input[["x.measure"]]
... ...
@@ -136,9 +127,6 @@ NULL
136 127
 }
137 128
 
138 129
 .norm_plot_args <- function(input){
139
-  if(missing(input)){
140
-    input <- list()
141
-  }
142 130
   if(!is.list(input)){
143 131
     stop("'plot.args' must be a list.")
144 132
   }
... ...
@@ -232,9 +220,9 @@ NULL
232 220
   colnames <- colnames[colnames != "labels"]
233 221
   data <- lapply(seq_along(colnames),
234 222
                  function(i){
235
-                   c <- colnames[i]
236
-                   c <- c("labels",c)
237
-                   d <- data[,c]
223
+                   cn <- colnames[i]
224
+                   cn <- c("labels",cn)
225
+                   d <- data[,cn]
238 226
                    colnames(d) <- c("labels","predictions")
239 227
                    d <- unlist(d)
240 228
                    rownames(d) <- NULL
... ...
@@ -246,8 +234,8 @@ NULL
246 234
 
247 235
 .get_prediction_data_ModifierSet <- function(x, coord, score){
248 236
   data <- lapply(x, .get_prediction_data_Modifier, coord, score)
249
-  names <- names(data[[1]])
250
-  data <- lapply(names,
237
+  data_names <- names(data[[1]])
238
+  data <- lapply(data_names,
251 239
                  function(name){
252 240
                    lapply(data,"[[",name)
253 241
                  })
... ...
@@ -260,7 +248,7 @@ NULL
260 248
                    list(predictions = predictions,
261 249
                         labels = labels)
262 250
                  })
263
-  names(data) <- names
251
+  names(data) <- data_names
264 252
   data
265 253
 }
266 254
 
... ...
@@ -289,7 +277,7 @@ NULL
289 277
     plot.args[["add"]] <- FALSE
290 278
   }
291 279
   #
292
-  mapply(
280
+  Map(
293 281
     function(d, name, colour, prediction.args, performance.args, plot.args){
294 282
       pred <- do.call(ROCR::prediction, c(list(predictions = d$predictions, 
295 283
                                                labels = d$labels), 
... ...
@@ -301,10 +289,10 @@ NULL
301 289
         stop("Error during plotting of performance object: ",tmp)
302 290
       }
303 291
       graphics::title(main = name)
304
-      if(plot.args[["abline"]] == TRUE){
292
+      if(plot.args[["abline"]]){
305 293
         graphics::abline(a = 0, b = 1)
306 294
       }
307
-      if(plot.args[["AUC"]] == TRUE){
295
+      if(plot.args[["AUC"]]){
308 296
         auc <- unlist(slot(performance(pred,"auc"),"y.values"))
309 297
         auc <- paste(c("AUC = "), round(auc,2L), sep = "")
310 298
         graphics::legend(0.55, 0.25, auc, bty = "n", cex = 1)
... ...
@@ -314,8 +302,7 @@ NULL
314 302
     names(data),
315 303
     MoreArgs = list(prediction.args = prediction.args,
316 304
                     performance.args = performance.args,
317
-                    plot.args = plot.args),
318
-    SIMPLIFY = FALSE)
305
+                    plot.args = plot.args))
319 306
   for(i in seq_len(n_remaining)){
320 307
     graphics::plot.new()
321 308
   }
... ...
@@ -328,11 +315,8 @@ NULL
328 315
 setMethod(
329 316
   f = "plotROC", 
330 317
   signature = signature(x = "Modifier"),
331
-  definition = function(x, coord, score = NULL, prediction.args, 
332
-                        performance.args, plot.args){
333
-    if(missing(score)){
334
-      score <- NULL
335
-    }
318
+  definition = function(x, coord, score = NULL, prediction.args = list(), 
319
+                        performance.args = list(), plot.args = list()){
336 320
     coord <- .norm_coord(coord, modType(x))
337 321
     data <- .get_prediction_data_Modifier(x, coord, score)
338 322
     .plot_ROCR(data,
... ...
@@ -348,11 +332,8 @@ setMethod(
348 332
 setMethod(
349 333
   f = "plotROC", 
350 334
   signature = signature(x = "ModifierSet"),
351
-  definition = function(x, coord, score = NULL, prediction.args,
352
-                        performance.args, plot.args){
353
-    if(missing(score)){
354
-      score <- NULL
355
-    }
335
+  definition = function(x, coord, score = NULL, prediction.args = list(), 
336
+                        performance.args = list(), plot.args = list()){
356 337
     coord <- .norm_coord(coord, modType(x))
357 338
     data <- .get_prediction_data_ModifierSet(x, coord, score)
358 339
     .plot_ROCR(data,
... ...
@@ -98,10 +98,10 @@ NULL
98 98
     lapply(x,
99 99
            function(z){
100 100
              data <- getAggregateData(z)
101
-             names <- .get_element_names(data, coord, args[["name"]],
101
+             element_names <- .get_element_names(data, coord, args[["name"]],
102 102
                                          args[["type"]])
103
-             data <- data[match(names, names(data))]
104
-             coord <- coord[match(names, names(coord))]
103
+             data <- data[match(element_names, names(data))]
104
+             coord <- coord[match(element_names, names(coord))]
105 105
              .perform_subset(data, coord, args[["flanking"]], 
106 106
                              args[["perTranscript"]])
107 107
            })
... ...
@@ -67,12 +67,12 @@ setMethod(f = "constructModRanges",
67 67
             if(any(length(positions) != data_length)){
68 68
               stop("Number of positions and scores do not match.")
69 69
             }
70
-            seqnames <- .get_unique_seqnames(range)
70
+            seqnames_unique <- .get_unique_seqnames(range)
71 71
             ranges <- IRanges::IRanges(start = positions,
72 72
                                        width = 1L)
73 73
             strand <- .get_unique_strand(range)
74 74
             mranges <- 
75
-              GenomicRanges::GRanges(seqnames = seqnames,
75
+              GenomicRanges::GRanges(seqnames = seqnames_unique,
76 76
                                      ranges = ranges,
77 77
                                      strand = strand,
78 78
                                      seqinfo = GenomeInfoDb::seqinfo(range),
... ...
@@ -2,15 +2,15 @@
2 2
 #' @include Modifier-class.R
3 3
 NULL
4 4
 
5
-#' @name visualizeData
6
-#' @aliases visualizeData visualizeDataByCoord getDataTrack
5
+#' @name plotData
6
+#' @aliases plotData plotDataByCoord getDataTrack
7 7
 #' 
8 8
 #' @title Visualizing data data from a \code{SequenceData}, 
9 9
 #' \code{SequenceDataSet}, \code{SequenceDataList}, \code{Modifier} or 
10 10
 #' \code{ModifierSet} object.
11 11
 #' 
12 12
 #' @description 
13
-#' With the \code{visualizeData} and \code{visualizeDataByCoord} functions data
13
+#' With the \code{plotData} and \code{plotDataByCoord} functions data
14 14
 #' from a \code{SequenceData}, \code{SequenceDataSet}, \code{SequenceDataList},
15 15
 #' \code{Modifier} or \code{ModifierSet} object can be visualized.
16 16
 #' 
... ...
@@ -27,9 +27,9 @@ NULL
27 27
 #' @param coord coordinates of a positions to subset to as a 
28 28
 #' \code{GRanges} object. The 'Parent' column is expected to match the 
29 29
 #' transcript name.
30
-#' @param name Only for \code{visualizeData}: the transcript name
31
-#' @param from Only for \code{visualizeData}: start position
32
-#' @param to Only for \code{visualizeData}: end position
30
+#' @param name Only for \code{plotData}: the transcript name
31
+#' @param from Only for \code{plotData}: start position
32
+#' @param to Only for \code{plotData}: end position
33 33
 #' @param type the data type of data show as data tracks.
34 34
 #' @param showSequenceData \code{TRUE} or \code{FALSE}: should the sequence data
35 35
 #' be shown? (default: \code{seqdata = FALSE})
... ...
@@ -60,14 +60,14 @@ NULL
60 60
 #' 
61 61
 #' @examples 
62 62
 #' data(msi,package="RNAmodR")
63
-#' visualizeData(msi[[1]], "2", from = 10L, to = 45L)
63
+#' plotData(msi[[1]], "2", from = 10L, to = 45L)
64 64
 #' \dontrun{
65
-#' visualizeData(msi, "2", from = 10L, to = 45L)
65
+#' plotData(msi, "2", from = 10L, to = 45L)
66 66
 #' }
67 67
 NULL
68 68
 
69 69
 .norm_show_argument <- function(show_arg, default = FALSE){
70
-  if(missing(show_arg) || !assertive::is_a_bool(show_arg)){
70
+  if(!assertive::is_a_bool(show_arg)){
71 71
     show_arg <- default
72 72
   }
73 73
   show_arg
... ...
@@ -143,23 +143,23 @@ NULL
143 143
 
144 144
 # ------------------------------------------------------------------------------
145 145
 
146
-#' @rdname visualizeData
146
+#' @rdname plotData
147 147
 setMethod(
148
-  f = "visualizeDataByCoord",
148
+  f = "plotDataByCoord",
149 149
   signature = signature(x = "Modifier", coord = "GRanges"),
150 150
   definition = function(x, coord, type = NA, window.size = 15L, ...) {
151 151
     # input check
152 152
     coord <- .norm_coord_for_visualization(ranges(x), coord)
153 153
     from_to <- .get_viz_from_to_coord(ranges(x), coord, window.size)
154
-    visualizeData(x, name = coord$Parent, from = from_to$from,
154
+    plotData(x, name = coord$Parent, from = from_to$from,
155 155
                   to = from_to$to, type = type, ...)
156 156
   }
157 157
 )
158 158
 
159
-#' @rdname visualizeData
159
+#' @rdname plotData
160 160
 #' @export
161 161
 setMethod(
162
-  f = "visualizeData",
162
+  f = "plotData",
163 163
   signature = signature(x = "Modifier"),
164 164
   definition = function(x, name, from, to, type = NA, showSequenceData = FALSE, 
165 165
                         showSequence = TRUE, showAnnotation = FALSE, ...) {
... ...
@@ -203,7 +203,7 @@ setMethod(
203 203
   }
204 204
 )
205 205
 
206
-#' @rdname visualizeData
206
+#' @rdname plotData
207 207
 #' @export
208 208
 setMethod(
209 209
   f = "getDataTrack",
... ...
@@ -174,9 +174,9 @@ setMethod(f = "relistToClass",
174 174
     return(FALSE)
175 175
   }
176 176
   namedRequired <- x[classNames %in% c("character","list")]
177
-  names <- unique(names(unlist(namedRequired)))
178
-  if(is.null(names) || 
179
-     !all(tolower(names) %in% c("treated","control"))){
177
+  namedRequired_names <- unique(names(unlist(namedRequired)))
178
+  if(is.null(namedRequired_names) || 
179
+     !all(tolower(namedRequired_names) %in% c("treated","control"))){
180 180
     return(FALSE)
181 181
   }
182 182
   x <- lapply(x,.norm_bamfiles)
... ...
@@ -193,27 +193,24 @@ setMethod(f = "relistToClass",
193 193
 
194 194
 #' @importFrom BiocParallel SerialParam register bpmapply bplapply
195 195
 .bamfiles_to_ModifierSet <- function(className, x, annotation, sequences,
196
-                                     seqinfo, ...){
196
+                                     seqinfo = NULL, ...){
197 197
   # check and normalize input
198 198
   args <- .norm_ModifierSet_args(list(...))
199 199
   className <- .norm_modifiertype(className)
200 200
   if(!is.list(x)){
201 201
     x <- list(x)
202 202
   }
203
-  names <- as.list(names(x))
204
-  if(length(names) == 0L){
205
-    names <- vector(mode = "list", length = length(x))
203
+  x_names <- as.list(names(x))
204
+  if(length(x_names) == 0L){
205
+    x_names <- vector(mode = "list", length = length(x))
206 206
   }
207 207
   x <- lapply(x, .norm_bamfiles, className)
208 208
   annotation <- .norm_annotation(annotation, className)
209 209
   annotation <- .load_annotation(annotation)
210 210
   sequences <- .norm_sequences(sequences, className)
211
-  if(missing(seqinfo)){
212
-    seqinfo <- NA
213
-  }
214 211
   ni <- seq_along(x)
215 212
   # choose were to use parallelization
216
-  if(args[["internalBP"]] == TRUE){
213
+  if(args[["internalBP"]]){
217 214
     BiocParallel::register(BiocParallel::SerialParam())
218 215
   }
219 216
   # do analysis by calling the Modifier classes
... ...
@@ -228,7 +225,7 @@ setMethod(f = "relistToClass",
228 225
       message(i,". ",className," analysis:")
229 226
     }
230 227
     # choose were to use parallelization
231
-    if(args[["internalBP"]] == FALSE){
228
+    if(!args[["internalBP"]]){
232 229
       BiocParallel::register(BiocParallel::SerialParam())
233 230
     }
234 231
     # do not pass this argument along to objects
... ...
@@ -243,7 +240,7 @@ setMethod(f = "relistToClass",
243 240
   PACKAGE <- getClass(className)@package
244 241
   CLASSFUN <- get(className)
245 242
   x <- BiocParallel::bpmapply(FUN,
246
-                              ni, x, names,
243
+                              ni, x, x_names,
247 244
                               MoreArgs = list(args = args, 
248 245
                                               className = className, 
249 246
                                               PACKAGE = PACKAGE,
... ...
@@ -253,9 +250,9 @@ setMethod(f = "relistToClass",
253 250
                                               seqinfo = seqinfo,
254 251
                                               ...),
255 252
                               SIMPLIFY = FALSE)
256
-  f <- vapply(names,is.null,logical(1))
257
-  names[f] <- as.list(as.character(seq_along(x))[f])
258
-  names(x) <- unlist(names)
253
+  f <- vapply(x_names,is.null,logical(1))
254
+  x_names[f] <- as.list(as.character(seq_along(x))[f])
255
+  names(x) <- unlist(x_names)
259 256
   # pass results to ModifierSet object
260 257
   .ModifierSet(className, x)
261 258
 }
... ...
@@ -267,7 +264,7 @@ setMethod(f = "relistToClass",
267 264
   elementType <- modifierType(x[[1]])
268 265
   className <- .get_classname_for_ModifierSet_from_modifier_type(className)
269 266
   if(className != .norm_classname_ModifierSet(elementType)){
270
-    stop("Something went wrong.")
267
+    stop("")
271 268
   }
272 269
   if (!all(vapply(x,
273 270
                   function(xi) extends(class(xi), elementType),
... ...
@@ -282,7 +279,7 @@ setMethod(f = "relistToClass",
282 279
 #' @export
283 280
 setGeneric( 
284 281
   name = "ModifierSet",
285
-  signature = c("x"),
282
+  signature = "x",
286 283
   def = function(className, x, annotation, sequences, seqinfo, ...)
287 284
     standardGeneric("ModifierSet")
288 285
 )
... ...
@@ -358,7 +355,7 @@ setMethod(
358 355
                                           optional = TRUE)))
359 356
     colnames(out) <- rep(" ",ncol(mf))
360 357
     if(is.null(names(object))){
361
-      rownames(out) <- c("| Modifications found:")
358
+      rownames(out) <- "| Modifications found:"
362 359
     } else {
363 360
       rownames(out) <- c("                      ",
364 361
                          "| Modifications found:")
... ...
@@ -469,26 +466,6 @@ setMethod(f = "seqinfo",
469 466
 )
470 467
 #' @rdname Modifier-functions
471 468
 #' @export
472
-setMethod(f = "settings", 
473
-          signature = signature(x = "ModifierSet"),
474
-          definition = function(x, name){
475
-            ans <- lapply(x,settings,name)
476
-            names(ans) <- names(x)
477
-            ans
478
-          }
479
-)
480
-#' @rdname Modifier-functions
481
-#' @export
482
-setReplaceMethod(f = "settings", 
483
-                 signature = signature(x = "ModifierSet"),
484
-                 definition = function(x, value){
485
-                   for(i in seq_along(x)){
486
-                     settings(x[[i]]) <- value
487
-                   }
488
-                   x
489
-                 })
490
-#' @rdname Modifier-functions
491
-#' @export
492 469
 setMethod(f = "sequences", 
493 470
           signature = signature(x = "ModifierSet"),
494 471
           definition = 
... ...
@@ -497,7 +474,7 @@ setMethod(f = "sequences",
497 474
                 stop("'modified' has to be a single logical value.",
498 475
                      call. = FALSE)
499 476
               }
500
-              if(modified == FALSE){
477
+              if(!modified){
501 478
                 return(sequences(sequenceData(x[[1]])))
502 479
               }
503 480
               mod <- .get_modifications_per_transcript(x)
... ...
@@ -512,6 +489,29 @@ setMethod(f = "sequences",
512 489
             }
513 490
 )
514 491
 
492
+# settings ---------------------------------------------------------------------
493
+
494
+#' @rdname settings
495
+#' @export
496
+setMethod(f = "settings", 
497
+          signature = signature(x = "ModifierSet"),
498
+          definition = function(x, name){
499
+            ans <- lapply(x,settings,name)
500
+            names(ans) <- names(x)
501
+            ans
502
+          }
503
+)
504
+#' @rdname settings
505
+#' @export
506
+setReplaceMethod(f = "settings", 
507
+                 signature = signature(x = "ModifierSet"),
508
+                 definition = function(x, value){
509
+                   for(i in seq_along(x)){
510
+                     settings(x[[i]]) <- value
511
+                   }
512
+                   x
513
+                 })
514
+
515 515
 # aggregate/modify -------------------------------------------------------------
516 516
 
517 517
 #' @rdname aggregate
... ...
@@ -84,8 +84,8 @@ NULL
84 84
       stop("Values in 'tx_id' have to be unique.",
85 85
            call. = FALSE)
86 86
     }
87
-    names <- names(ranges(x))
88
-    if(!all(alias$tx_id %in% names)){
87
+    ranges_names <- names(ranges(x))
88
+    if(!all(alias$tx_id %in% ranges_names)){
89 89
       stop("All values in 'tx_id' have to be valid transcript ids used as ",
90 90
            "names for the data.", call. = FALSE)
91 91
     }
... ...
@@ -161,10 +161,10 @@ NULL
161 161
   coord <- coord[match(names(data), names(coord))]
162 162
   # keep rownames/names and unlist data
163 163
   positions <- rownames(data)
164
-  names <- as.character(S4Vectors::Rle(names(data), lengths(data)))
164
+  data_names <- as.character(S4Vectors::Rle(names(data), lengths(data)))
165 165
   data <- unlist(data)
166 166
   # add names and positions column as factors
167
-  data$names <- factor(names)
167
+  data$names <- factor(data_names)
168 168
   data$positions <- factor(as.integer(unlist(positions)))
169 169
   rownames(data) <- NULL
170 170
   # add activity information if present
... ...
@@ -245,7 +245,6 @@ setMethod("compareByCoord",
245 245
 )
246 246
 
247 247
 .normlize_data_against_one_sample <- function(data, normalize){
248
-  
249 248
   if(!missing(normalize)){
250 249
     colnames <- colnames(data)
251 250
     colnames <- colnames[!(colnames %in% c("positions","names","mod","Activity"))]
... ...
@@ -260,7 +259,7 @@ setMethod("compareByCoord",
260 259
         data[,normalize]
261 260
     } else if(is.logical(normalize)){
262 261
       assertive::assert_is_a_bool(normalize)
263
-      if(normalize == TRUE){
262
+      if(normalize){
264 263
         data[,colnames] <- as.data.frame(data[,colnames,drop = FALSE]) - 
265 264
           apply(data[,colnames],1,max)
266 265
       }
... ...
@@ -289,10 +288,10 @@ setMethod("compareByCoord",
289 288
   if(is.factor(positions)){
290 289
     positions <- as.numeric(as.character(positions))
291 290
   }
292
-  list <- list(as.character(positions),
293
-               mod,
294
-               activity)
295
-  spacer <- lapply(list,
291
+  tmp <- list(as.character(positions),
292
+              mod,
293
+              activity)
294
+  spacer <- lapply(tmp,
296 295
                    function(el){
297 296
                      if(is.null(el)) return(NULL)
298 297
                      length <- nchar(el)
... ...
@@ -302,15 +301,15 @@ setMethod("compareByCoord",
302 301
                                      paste0(rep(" ",n),collapse = "")
303 302
                                    }))
304 303
                    })
305
-  sep <- lapply(seq_along(list),
304
+  sep <- lapply(seq_along(tmp),
306 305
                    function(i){
307 306
                      if(i > 1L){
308
-                       rep(" - ",length(list[[i]]))
307
+                       rep(" - ",length(tmp[[i]]))
309 308
                      } else {
310
-                       rep("",length(list[[i]]))
309
+                       rep("",length(tmp[[i]]))
311 310
                      }
312 311
                    })
313
-  labels <- mapply(paste0, spacer, list, sep, SIMPLIFY = FALSE)
312
+  labels <- Map(paste0, spacer, tmp, sep)
314 313
   labels <- Reduce(paste0, rev(labels))
315 314
   f <- factor(labels, levels = unique(labels))
316 315
   stats::reorder(f,positions)
... ...
@@ -32,7 +32,7 @@ NULL
32 32
 }
33 33
 
34 34
 .add_viz_colours <- function(dts, colours){
35
-  dts <- mapply(
35
+  dts <- Map(
36 36
     function(dt, colour){
37 37
       if(is.list(dt)){
38 38
         dt <- lapply(dt,
... ...
@@ -48,13 +48,12 @@ NULL
48 48
       dt
49 49
     },
50 50
     dts,
51
-    colours,
52
-    SIMPLIFY = FALSE)
51
+    colours)
53 52
   dts
54 53
 }
55 54
 
56 55
 .add_viz_names <- function(dts, names){
57
-  dts <- mapply(
56
+  dts <- Map(
58 57
     function(dt, name){
59 58
       if(is.list(dt)){
60 59
         dt <- lapply(dt,
... ...
@@ -68,8 +67,7 @@ NULL
68 67
       dt
69 68
     },
70 69
     dts,
71
-    names,
72
-    SIMPLIFY = FALSE)
70
+    names)
73 71
   dts
74 72
 }
75 73
 
... ...
@@ -94,7 +92,7 @@ NULL
94 92
       max
95 93
     })
96 94
   names(max) <- types
97
-  dts <- mapply(
95
+  dts <- Map(
98 96
     function(dt,t){
99 97
       ylim <- c(0,max[[t]])
100 98
       if(sum(ylim) != 0L){
... ...
@@ -107,25 +105,25 @@ NULL
107 105
   dts
108 106
 }
109 107
 
110
-#' @rdname visualizeData
108
+#' @rdname plotData
111 109
 #' @export
112 110
 setMethod(
113
-  f = "visualizeDataByCoord",
111
+  f = "plotDataByCoord",
114 112
   signature = signature(x = "ModifierSet", coord = "GRanges"),
115 113
   definition = function(x, coord, type = NA, window.size = 15L, ...) {
116 114
     # input check
117 115
     coord <- .norm_coord_for_visualization(ranges(x), coord)
118 116
     from_to <- .get_viz_from_to_coord(ranges(x), coord, window.size)
119
-    visualizeData(x, name = coord$Parent, from = from_to$from,
117
+    plotData(x, name = coord$Parent, from = from_to$from,
120 118
                   to = from_to$to, type = type, ...)
121 119
     
122 120
   }
123 121
 )
124 122
 
125
-#' @rdname visualizeData
123
+#' @rdname plotData
126 124
 #' @export
127 125
 setMethod(
128
-  f = "visualizeData",
126
+  f = "plotData",
129 127
   signature = signature(x = "ModifierSet"),
130 128
   definition = function(x, name, from, to, type = NA, showSequenceData = FALSE, 
131 129
                         showSequence = TRUE, showAnnotation = FALSE, ...) {
... ...
@@ -35,12 +35,12 @@ NULL
35 35
 }
36 36
 
37 37
 .merge_summary_data <- function(bamfilesstats,datastats){
38
-  names <- c(rownames(bamfilesstats),rownames(datastats))
38
+  bf_d_names <- c(rownames(bamfilesstats),rownames(datastats))
39 39
   stats <- data.frame(mapply(c,
40 40
                              as.list(bamfilesstats),
41 41
                              as.list(datastats)),
42 42
                       stringsAsFactors = FALSE)
43
-  rownames(stats) <- names
43
+  rownames(stats) <- bf_d_names
44 44
   colnames(stats) <- colnames(bamfilesstats)
45 45
   stats
46 46
 }
... ...
@@ -161,9 +161,9 @@ NULL
161 161
 #' \code{findMod} for each \code{Modifier} class. See also 
162 162
 #' \code{\link[=modify]{findMod}}.
163 163
 #' 
164
-#' \code{visualizeData}/\code{visualizeDataByCoord} for each \code{Modifier} 
164
+#' \code{plotData}/\code{plotDataByCoord} for each \code{Modifier} 
165 165
 #' and \code{ModifierSet} class. See also 
166
-#' \code{\link[=visualizeData]{visualizeData}}.
166
+#' \code{\link[=plotData]{plotData}}.
167 167
 #' 
168 168
 #' The following helper function can be called from within \code{findMod} to
169 169
 #' construct a coordinate for each modification found:
... ...
@@ -232,7 +232,7 @@ NULL
232 232
 #' )
233 233
 #' setMethod(
234 234
 #'   f = "getDataTrack",
235
-#'   signature = signature(x = "ExampleSequenceData"),
235
+#'   signature = c(x = "ExampleSequenceData"),
236 236
 #'   definition = function(x, name, ...) {
237 237
 #'     ###
238 238
 #'   }
... ...
@@ -240,7 +240,7 @@ NULL
240 240
 #' 
241 241
 #' # new Modifier class
242 242
 #' setClass("ModExample",
243
-#'          contains = c("Modifier"),
243
+#'          contains = "Modifier",
244 244
 #'          prototype = list(mod = "X",
245 245
 #'                           score = "score",
246 246
 #'                           dataType = "ExampleSequenceData"))
... ...
@@ -250,7 +250,7 @@ NULL
250 250
 #' }
251 251
 #' 
252 252
 #' setMethod(f = "aggregateData",
253
-#'           signature = signature(x = "ModExample"),
253
+#'           signature = c(x = "ModExample"),
254 254
 #'           definition =
255 255
 #'             function(x, force = FALSE){
256 256
 #'               # Some data with element per transcript
... ...
@@ -270,13 +270,13 @@ NULL
270 270
 #'   }
271 271
 #' )
272 272
 #' setMethod(
273
-#'   f = "visualizeDataByCoord",
273
+#'   f = "plotDataByCoord",
274 274
 #'   signature = signature(x = "ModExample", coord = "GRanges"),
275 275
 #'   definition = function(x, coord, type = "score", window.size = 15L, ...) {
276 276
 #'   }
277 277
 #' )
278 278
 #' setMethod(
279
-#'   f = "visualizeData",
279
+#'   f = "plotData",
280 280
 #'   signature = signature(x = "ModExample"),
281 281
 #'   definition = function(x, name, from, to, type = "score", ...) {
282 282
 #'   }
... ...
@@ -292,13 +292,13 @@ NULL
292 292
 #' }
293 293
 #' 
294 294
 #' setMethod(
295
-#'   f = "visualizeDataByCoord",
295
+#'   f = "plotDataByCoord",
296 296
 #'   signature = signature(x = "ModSetExample", coord = "GRanges"),
297 297
 #'   definition = function(x, coord, type = "score", window.size = 15L, ...) {
298 298
 #'   }
299 299
 #' )
300 300
 #' setMethod(
301
-#'   f = "visualizeData",
301
+#'   f = "plotData",
302 302
 #'   signature = signature(x = "ModSetExample"),
303 303
 #'   definition = function(x, name, from, to, type = "score", ...) {
304 304
 #'   }
... ...
@@ -458,7 +458,7 @@ setMethod("rownames", "SequenceData",
458 458
     }
459 459
     data <- do.call(cbind,data)
460 460
   } else {
461
-    stop("Something went wrong.")
461
+    stop("")
462 462
   }
463 463
   data
464 464
 }
... ...
@@ -490,8 +490,8 @@ setMethod("rownames", "SequenceData",
490 490
   ##############################################################################
491 491
   # setup additional variables
492 492
   ##############################################################################
493
-  if(missing(args) || !is.list(args)){
494
-    args <- list()
493
+  if(!is.list(args)){
494
+    args <- as.list(args)
495 495
   }
496 496
   proto <- new(className)
497 497
   minQuality <- .norm_min_quality(args, proto@minQuality)
... ...
@@ -545,7 +545,7 @@ setMethod("rownames", "SequenceData",
545 545
   names(data) <- names(ranges)
546 546
   if(any(names(ranges) != names(sequences)) || 
547 547
      any(names(ranges) != names(data))){
548
-    stop("Something went wrong.")
548
+    stop("")
549 549
   }
550 550
   message("OK")
551 551
   ##############################################################################
... ...
@@ -62,13 +62,12 @@ CoverageSequenceData <- function(bamfiles, annotation, sequences, seqinfo, ...){
62 62
   coverage <- as(coverage,"IntegerList")
63 63
   # subset per transcript
64 64
   seqs <- .seqs_rl_strand(grl, force_continous = TRUE)
65
-  coverage <- IRanges::IntegerList(mapply(
65
+  coverage <- IRanges::IntegerList(Map(
66 66
     function(gr,s){
67 67
       coverage[[unique(GenomicRanges::seqnames(gr))]][s]
68 68
     },
69 69
     grl,
70
-    seqs,
71
-    SIMPLIFY = FALSE))
70
+    seqs))
72 71
   coverage
73 72
 }
74 73
 
... ...
@@ -24,7 +24,7 @@ NULL
24 24
 #' \code{\link[=SequenceData-functions]{SequenceData-functions}}
25 25
 #' @param x a \code{End5SequenceData}, \code{End3SequenceData} or
26 26
 #' \code{EndSequenceData} object
27
-#' @param name For \code{\link[=visualizeDataByCoord]{getDataTrack}}: a valid
27
+#' @param name For \code{\link[=plotDataByCoord]{getDataTrack}}: a valid
28 28
 #' transcript name. Must be a name of \code{ranges(x).}
29 29
 #' @param condition For \code{\link{aggregate}}: condition for which the data
30 30
 #' should be aggregated.
... ...
@@ -175,7 +175,7 @@ EndSequenceData <- function(bamfiles, annotation, sequences, seqinfo, ...){
175 175
   # calculate tables and add empty positions
176 176
   # also remove overhanging read data
177 177
   seqs <- .seqs_rl(grl)
178
-  data <- IRanges::IntegerList(mapply(
178
+  data <- IRanges::IntegerList(Map(
179 179
     function(d,s){
180 180
       bg <- table(s) - 1L
181 181
       d <- d[d %in% s]
... ...
@@ -189,16 +189,14 @@ EndSequenceData <- function(bamfiles, annotation, sequences, seqinfo, ...){
189 189
       as.integer(d)
190 190
     },
191 191
     data,
192
-    seqs[f],
193
-    SIMPLIFY = FALSE))
192
+    seqs[f]))
194 193
   # get data for empty transcripts
195
-  data_not_found <- IRanges::IntegerList(mapply(
194
+  data_not_found <- IRanges::IntegerList(Map(
196 195
     function(s){
197 196
       d <- table(s) - 1
198 197
       as.integer(d)
199 198
     },
200
-    seqs[f_not_found],
201
-    SIMPLIFY = FALSE))
199
+    seqs[f_not_found]))
202 200
   # merge and order
203 201
   data <- c(data,data_not_found)
204 202
   data <- data[match(names(grl),names(data))]
... ...
@@ -27,7 +27,7 @@ NULL
27 27
 #' \code{\link[=SequenceData-class]{SequenceData}} and
28 28
 #' \code{\link[=SequenceData-functions]{SequenceData-functions}}
29 29
 #' @param x a \code{CoverageSequenceData}
30
-#' @param name For \code{\link[=visualizeDataByCoord]{getDataTrack}}: a valid 
30
+#' @param name For \code{\link[=plotDataByCoord]{getDataTrack}}: a valid 
31 31
 #' transcript name. Must be a name of \code{ranges(x)}
32 32
 #' @param condition For \code{\link{aggregate}}: condition for which the data 
33 33
 #' should be aggregated.
... ...
@@ -126,7 +126,7 @@ setMethod("summary",
126 126
   enddata <- .summarize_to_position_data(data, strands_u[f], type)
127 127
   # tabulate the counts per position
128 128
   seqs <- .seqs_rl_strand(grl, force_continous = TRUE)
129
-  enddata <- IRanges::IntegerList(mapply(
129
+  enddata <- IRanges::IntegerList(Map(
130 130
     function(d,s){
131 131
       bg <- table(s) - 1L
132 132
       d <- d[d %in% s]
... ...
@@ -140,12 +140,11 @@ setMethod("summary",
140 140
       as.integer(d)
141 141
     },
142 142
     enddata,
143
-    seqs[f],
144
-    SIMPLIFY = FALSE))
143
+    seqs[f]))
145 144
   # noralize against total number transcript or against the overlap per position
146 145
   normTranscript <- (enddata / lengths(data)) * 1000
147 146
   normTranscript <- IRanges::NumericList(lapply(normTranscript,unname))
148
-  normOverlap <- IRanges::NumericList(mapply(
147
+  normOverlap <- IRanges::NumericList(Map(
149 148
     function(d,end,pos){
150 149
       gr <- GenomicRanges::GRanges(
151 150
         seqnames = as.character(unique(seqnames(d))),
... ...
@@ -155,16 +154,14 @@ setMethod("summary",
155 154
     },
156 155
     data,
157 156
     enddata,
158
-    seqs[f],
159
-    SIMPLIFY = FALSE))
157
+    seqs[f]))
160 158
   # calculate tables and add empty positions
161
-  data_not_found <- IRanges::IntegerList(mapply(
159
+  data_not_found <- IRanges::IntegerList(Map(
162 160
     function(s){
163 161
       d <- table(s) - 1
164 162
       as.integer(d)
165 163
     },
166
-    seqs[f_not_found],
167
-    SIMPLIFY = FALSE))
164
+    seqs[f_not_found]))
168 165
   # merge data with empty data and order based on factor numbers
169 166
   enddata <- c(enddata,data_not_found)
170 167
   enddata@unlistData[is.na(enddata@unlistData)] <- 0L
... ...
@@ -24,7 +24,7 @@ NULL
24 24
 #' \code{\link[=SequenceData-class]{SequenceData}} and
25 25
 #' \code{\link[=SequenceData-functions]{SequenceData-functions}}
26 26
 #' @param x a \code{PileupSequenceData}
27
-#' @param name For \code{\link[=visualizeDataByCoord]{getDataTrack}}: a valid 
27
+#' @param name For \code{\link[=plotDataByCoord]{getDataTrack}}: a valid 
28 28
 #' transcript name. Must be a name of \code{ranges(x)}
29 29
 #' @param condition For \code{\link{aggregate}}: condition for which the data 
30 30
 #' should be aggregated.
... ...
@@ -138,7 +138,7 @@ PileupSequenceData <- function(bamfiles, annotation, sequences, seqinfo, ...){
138 138
   # object and using it to relist
139 139
   pileup <- .splitPileupAsList_transcript(pileup, grl)
140 140
   if(length(pileup) != length(grl)){
141
-    stop("Something went wrong.")
141
+    stop("")
142 142
   }
143 143
   # sanitize pilup data
144 144
   # - keep only data for correct strand
... ...
@@ -146,7 +146,7 @@ PileupSequenceData <- function(bamfiles, annotation, sequences, seqinfo, ...){
146 146
   strands_u <- .get_strand_u_GRangesList(grl)
147 147
   seqs <- .seqs_rl(grl)
148 148
   pileup <- IRanges::SplitDataFrameList(
149
-    mapply(
149
+    Map(
150 150
       function(d,seq,strand){
151 151
         ans <- NULL
152 152
         d <- d[d$strand == strand,]
... ...
@@ -165,8 +165,7 @@ PileupSequenceData <- function(bamfiles, annotation, sequences, seqinfo, ...){
165 165
       },
166 166
       pileup,
167 167
       seqs,
168
-      strands_u,
169
-      SIMPLIFY = FALSE))
168
+      strands_u))
170 169
   names(pileup) <- names(grl)
171 170
   pileup
172 171
 }
... ...
@@ -394,7 +393,7 @@ setMethod(
394 393
 #' @rdname PileupSequenceData-class
395 394
 #' @export
396 395
 setGeneric(name = "pileupToCoverage",
397
-           signature = c("x"),
396
+           signature = "x",
398 397
            def = function(x) standardGeneric("pileupToCoverage"))
399 398
 
400 399
 .aggregate_pile_up_to_coverage <- function(data){
... ...
@@ -34,7 +34,7 @@ RNAMODR_PROT_SEQDATA_PLOT_DATA_COLOURS <- c(means = "#FBB4AE",
34 34
 #' \code{\link[=SequenceData-class]{SequenceData}} and
35 35
 #' \code{\link[=SequenceData-functions]{SequenceData-functions}}
36 36
 #' @param x a \code{ProtectedEndSequenceData}
37
-#' @param name For \code{\link[=visualizeDataByCoord]{getDataTrack}}: a valid 
37
+#' @param name For \code{\link[=plotDataByCoord]{getDataTrack}}: a valid 
38 38
 #' transcript name. Must be a name of \code{ranges(x)}
39 39
 #' @param condition For \code{\link{aggregate}}: condition for which the data 
40 40
 #' should be aggregated.
... ...
@@ -95,7 +95,7 @@ NULL
95 95
     coord <- coord[!duplicated(coord)]
96 96
     return(.norm_coord(coord, type, merge))
97 97
   } else {
98
-    stop("Something went wrong.")
98
+    stop("")
99 99
   }
100 100
   if(unique(unlist(width(ranges(coord)))) != 1L){
101 101
     stop("Elements with a width != 1L are not supported.",
... ...
@@ -132,30 +132,29 @@ NULL
132 132
                           paste(type, collapse = "','"), "'")
133 133
   }
134 134
   if(is.na(name)){
135
-    names <- intersect(namesData, namesCoord)
135
+    intersect_names <- intersect(namesData, namesCoord)
136 136
     message <- c("No intersection between names in data of 'x' and Parent in ",
137 137
                  "'coord'\n ",messageType)
138 138
   } else {
139
-    names <- Reduce(intersect,
140
-                    list(namesData,namesCoord),name)
139
+    intersect_names <- Reduce(intersect,
140
+                              list(namesData,namesCoord),name)
141 141
     message <- c("No intersection between names in data of 'x', Parent in ",
142 142
                  "'coord'\n ",messageType," and the selected name.")
143 143
   }
144
-  if(length(names) == 0L){
144
+  if(length(intersect_names) == 0L){
145 145
     stop(message,
146 146
          call. = FALSE)
147 147
   }
148
-  names
148
+  intersect_names
149 149
 }
150 150
 
151 151
 .check_for_invalid_positions <- function(data, coord){
152 152
   lengths <- lengths(data)
153 153
   positions <- start(ranges(coord))
154 154
   f_names <- match(names(positions),names(lengths))
155
-  f <- IRanges::LogicalList(mapply(function(i,j){i >= j},
156
-                                   positions,
157
-                                   lengths[f_names],
158
-                                   SIMPLIFY = FALSE))
155
+  f <- IRanges::LogicalList(Map(function(i,j){i >= j},
156
+                                positions,
157
+                                lengths[f_names]))
159 158
   if(!any(lengths(BiocGenerics::which(f)) > 0L )){
160 159
     return(NULL)
161 160
   }
... ...
@@ -203,13 +202,12 @@ NULL
203 202
                                     flank))
204 203
   ans <- data[m][ff]
205 204
   if(perTranscript){
206
-    pos <- IRanges::CharacterList(mapply(
205
+    pos <- IRanges::CharacterList(Map(
207 206
       function(d,i){
208 207
         BiocGenerics::which(rownames(d) %in% i)
209 208
       },
210 209
       data[m],
211
-      flank,
212
-      SIMPLIFY = FALSE))
210
+      flank))
213 211
     rownames(ans) <- pos
214 212
   }
215 213
   return(ans)
... ...
@@ -221,9 +219,10 @@ NULL
221 219
   args <- .norm_subset_args(list(...), NULL)
222 220
   data <- .norm_data(data)
223 221
   coord <- .norm_coord(coord, NA, args[["merge"]])
224
-  names <- .get_element_names(data, coord, args[["name"]], args[["type"]])
225
-  data <- data[match(names, names(data))]
226
-  coord <- coord[names(coord) %in% names]
222
+  element_names <- .get_element_names(data, coord, args[["name"]],
223
+                                      args[["type"]])
224
+  data <- data[match(element_names, names(data))]
225
+  coord <- coord[names(coord) %in% element_names]
227 226
   .perform_subset(data, coord, args[["flanking"]], args[["perTranscript"]])
228 227
 }
229 228
 
... ...
@@ -237,9 +236,10 @@ NULL
237 236
     data <- .norm_aggregate_data(aggregate(x))
238 237
   }
239 238
   data <- .norm_data(data)
240
-  names <- .get_element_names(data, coord, args[["name"]], args[["type"]])
241
-  data <- data[match(names, names(data))]
242
-  coord <- coord[names(coord) %in% names]
239
+  element_names <- .get_element_names(data, coord, args[["name"]],
240
+                                      args[["type"]])
241
+  data <- data[match(element_names, names(data))]
242
+  coord <- coord[names(coord) %in% element_names]
243 243
   .perform_subset(data, coord, args[["flanking"]], args[["perTranscript"]])
244 244
 }
245 245
 
... ...
@@ -266,7 +266,7 @@ NULL
266 266
              } else if(is(z,"SequenceDataSet")) {
267 267
                return(.subset_SequenceDataSet_by_GRangesList(z, coord, ...))
268 268
              } else {
269
-               stop("Something went wrong.")
269
+               stop("")
270 270
              }
271 271
            })
272 272
   ans <- do.call(cbind,ans)
... ...
@@ -346,10 +346,9 @@ setMethod("subsetByCoord",
346 346
   }
347 347
   labels <- IRanges::LogicalList(lapply(lengths(data),
348 348
                                         function(l){rep(FALSE,l)}))
349
-  labels[f_rn] <- IRanges::LogicalList(mapply("%in%",
350
-                                              rn_d[f_rn],
351
-                                              positions[f_p],
352
-                                              SIMPLIFY = FALSE))
349
+  labels[f_rn] <- IRanges::LogicalList(Map("%in%",
350
+                                           rn_d[f_rn],
351
+                                           positions[f_p]))
353 352
   unlisted_data <- unlist(data, use.names = FALSE)
354 353
   unlisted_data$labels <- unlist(labels, use.names = FALSE)
355 354
   return(relist(unlisted_data, data))
... ...
@@ -407,7 +406,7 @@ setMethod("subsetByCoord",
407 406
              } else if(is(z,"SequenceDataSet")) {
408 407
                return(.label_SequenceDataSet_by_GRangesList(z, coord,...))
409 408
              } else {
410
-               stop("Something went wrong.")
409
+               stop("")
411 410
              }
412 411
            })
413 412
   .keep_one_labels_column(ans)
... ...
@@ -28,13 +28,6 @@ NULL
28 28
   window.size
29 29
 }
30 30
 
31
-.norm_viz_name <- function(name){
32
-  if(missing(name)){
33
-    name <- NULL
34
-  }
35
-  name
36
-}
37
-
38 31
 .get_viz_from_to_coord <- function(ranges, coord, window.size){
39 32
   window.size <- .norm_viz_windows.size(window.size)
40 33
   start <- start(coord) - window.size
... ...
@@ -185,8 +178,8 @@ NULL
185 178
   if(length(ranges) == 0L){
186 179
     stop("No ranges with seqnames = '",chromosome,"' found.")
187 180
   }
188
-  names <- names(ranges)
189
-  seq <- seq[names(seq) %in% names]
181
+  ranges_names <- names(ranges)
182
+  seq <- seq[names(seq) %in% ranges_names]
190 183
   if(length(seq) == 0L){
191 184
     stop("No sequences for seqnames = '",chromosome,"' found.")
192 185
   }
... ...
@@ -268,7 +261,7 @@ NULL
268 261
   } else if(is(seq,"ModRNAStringSet")){
269 262
     st <- FUN("ModRNASequenceTrack","ModRNAStringSet", seq, args)
270 263
   } else {
271
-    stop("Something went wrong.")
264
+    stop("")
272 265
   }
273 266
   st
274 267
 }
... ...
@@ -288,14 +281,14 @@ NULL
288 281
     x <- x[name]
289 282
     data <- aggregate(x)
290 283
   } else {
291
-    stop("Something went wrong.")
284
+    stop("")
292 285
   }
293 286
   strand_u <- .get_strand_u_GRangesList(ranges)
294 287
   seqs <- .seqs_rl(ranges)
295 288
   seqs[strand_u == "-"] <- rev(seqs[strand_u == "-"])
296
-  seqnames <- .seqnames_rl(ranges)
289
+  ranges_seqnames <- .seqnames_rl(ranges)
297 290
   strands <- .strands_rl(ranges)
298
-  ans <- GenomicRanges::GRanges(seqnames = unlist(seqnames),
291
+  ans <- GenomicRanges::GRanges(seqnames = unlist(ranges_seqnames),
299 292
                                 ranges = IRanges::IRanges(start = unlist(seqs),
300 293
                                                           width = 1),
301 294
                                 strand = unlist(strands),
... ...
@@ -307,25 +300,25 @@ NULL
307 300
 
308 301
 ################################################################################
309 302
 
310
-#' @rdname visualizeData
303
+#' @rdname plotData
311 304
 #' @export
312 305
 setMethod(
313
-  f = "visualizeDataByCoord",
306
+  f = "plotDataByCoord",
314 307
   signature = signature(x = "SequenceData", coord = "GRanges"),
315 308
   definition = function(x, coord, type = NA, window.size = 15L, ...) {
316 309
     # input check
317 310
     coord <- .norm_coord_for_visualization(ranges(x), coord)
318 311
     from_to <- .get_viz_from_to_coord(ranges(x), coord, window.size)
319
-    visualizeData(x, name = coord$Parent, from = from_to$from,
312
+    plotData(x, name = coord$Parent, from = from_to$from,
320 313
                   to = from_to$to, type = type, ...)
321 314
   }
322 315
 )
323 316
 
324
-#' @rdname visualizeData
317
+#' @rdname plotData
325 318
 #' @importFrom Gviz plotTracks
326 319
 #' @export
327 320
 setMethod(
328
-  f = "visualizeData",
321
+  f = "plotData",
329 322
   signature = signature(x = "SequenceData"),
330 323
   definition = function(x, name, from, to, perTranscript = FALSE, 
331 324
                         showSequence = TRUE, showAnnotation = FALSE, ...) {
... ...
@@ -358,7 +351,7 @@ setMethod(
358 351
   }
359 352
 )
360 353
 
361
-#' @rdname visualizeData
354
+#' @rdname plotData
362 355
 #' @export
363 356
 setMethod(
364 357
   f = "getDataTrack",
... ...
@@ -31,7 +31,7 @@ NULL
31 31
 #' @rdname SequenceDataList-class
32 32
 #' @export
33 33
 setClass("SequenceDataList",
34
-         contains = c("List"),
34
+         contains = "List",
35 35
          slots = c(listData = "list"),
36 36
          prototype = list(elementType = "SD_or_SDS"))
37 37
 
... ...
@@ -2,7 +2,7 @@
2 2
 #' @include SequenceDataSet-class.R
3 3
 NULL
4 4
 
5
-#' @rdname visualizeData
5
+#' @rdname plotData
6 6
 #' @export
7 7
 setMethod(
8 8
   f = "getDataTrack",
... ...
@@ -18,25 +18,25 @@ setMethod(
18 18
 )
19 19
 
20 20
 
21
-#' @rdname visualizeData
21
+#' @rdname plotData
22 22
 #' @export
23 23
 setMethod(
24
-  f = "visualizeDataByCoord",
24
+  f = "plotDataByCoord",
25 25
   signature = signature(x = "SequenceDataList", coord = "GRanges"),
26 26
   definition = function(x, coord, type = NA, window.size = 15L, ...) {
27 27
     # input check
28 28
     coord <- .norm_coord_for_visualization(ranges(x), coord)
29 29
     from_to <- .get_viz_from_to_coord(ranges(x), coord, window.size)
30
-    visualizeData(x, name = coord$Parent, from = from_to$from,
30
+    plotData(x, name = coord$Parent, from = from_to$from,
31 31
                   to = from_to$to, type = type, ...)
32 32
   }
33 33
 )
34 34
 
35
-#' @rdname visualizeData
35
+#' @rdname plotData
36 36
 #' @importFrom Gviz plotTracks
37 37
 #' @export
38 38
 setMethod(
39
-  f = "visualizeData",
39
+  f = "plotData",
40 40
   signature = signature(x = "SequenceDataList"),
41 41
   definition = function(x, name, from, to, perTranscript = FALSE, 
42 42
                         showSequence = TRUE, showAnnotation = FALSE, ...) {
... ...
@@ -30,7 +30,7 @@ NULL
30 30
 #' @rdname SequenceDataSet-class
31 31
 #' @export
32 32
 setClass("SequenceDataSet",
33
-         contains = c("List"),
33
+         contains = "List",
34 34
          slots = c(listData = "list"),
35 35
          prototype = list(elementType = "SequenceData"))
36 36
 
... ...
@@ -2,7 +2,7 @@
2 2
 #' @include SequenceDataSet-class.R
3 3
 NULL
4 4
 
5
-#' @rdname visualizeData
5
+#' @rdname plotData
6 6
 #' @export
7 7
 setMethod(
8 8
   f = "getDataTrack",
... ...
@@ -18,25 +18,25 @@ setMethod(
18 18
 )
19 19
 
20 20
 
21
-#' @rdname visualizeData
21
+#' @rdname plotData
22 22
 #' @export
23 23
 setMethod(
24
-  f = "visualizeDataByCoord",
24
+  f = "plotDataByCoord",
25 25
   signature = signature(x = "SequenceDataSet", coord = "GRanges"),
26 26
   definition = function(x, coord, type = NA, window.size = 15L, ...) {
27 27
     # input check
28 28
     coord <- .norm_coord_for_visualization(ranges(x), coord)
29 29
     from_to <- .get_viz_from_to_coord(ranges(x), coord, window.size)
30
-    visualizeData(x, name = coord$Parent, from = from_to$from,
30
+    plotData(x, name = coord$Parent, from = from_to$from,
31 31
                   to = from_to$to, type = type, ...)
32 32
   }
33 33
 )
34 34
 
35
-#' @rdname visualizeData
35
+#' @rdname plotData
36 36
 #' @importFrom Gviz plotTracks
37 37
 #' @export
38 38
 setMethod(
39
-  f = "visualizeData",
39
+  f = "plotData",
40 40
   signature = signature(x = "SequenceDataSet"),
41 41
   definition = function(x, name, from, to, perTranscript = FALSE, 
42 42
                         showSequence = TRUE, showAnnotation = FALSE, ...) {
... ...
@@ -123,8 +123,8 @@ SAMPLE_TYPES <- c("treated","control")
123 123
     stop("Names of BamFileList must either be 'treated' or 'control' (case ",
124 124
          "insensitive). No names found.")
125 125
   }
126
-  names <- tolower(unique(names(x)))
127
-  if(!all(names %in% SAMPLE_TYPES)){
126
+  x_names <- tolower(unique(names(x)))
127
+  if(!all(x_names %in% SAMPLE_TYPES)){
128 128
     stop("Names of BamFileList must either be 'treated' or 'control' (case ",
129 129
          "insensitive).",
130 130
          call. = FALSE)
... ...
@@ -185,9 +185,12 @@ SAMPLE_TYPES <- c("treated","control")
185 185
 #' @importFrom BSgenome seqnames
186 186
 #' @importFrom Rsamtools scanFa
187 187
 .norm_seqnames <- function(bamfiles, annotation, sequences, seqinfo, className){
188
+  if(missing(seqinfo)){
189
+    seqinfo <- NULL
190
+  }
188 191
   # norm seqinfo
189
-  if(missing(seqinfo) || 
190
-     (!is(seqinfo,"Seqinfo") && (is.na(seqinfo) || is.null(seqinfo)))){
192
+  if(is.null(seqinfo) || 
193
+     (!is(seqinfo,"Seqinfo") && (is.na(seqinfo)))){
191 194
     seqinfo <- .bam_header_to_seqinfo(bamfiles)
192 195
   }
193 196
   if(!is(seqinfo,"Seqinfo") && 
... ...
@@ -199,19 +202,21 @@ SAMPLE_TYPES <- c("treated","control")
199 202
   }
200 203
   # norm annotation
201 204
   if(!is(annotation,"GRangesList") & !is(annotation,"TxDb")){
202
-    stop("Something went wrong.")
205
+    stop("")
203 206
   }
204 207
   if(!is(sequences,"FaFile") & !is(sequences,"BSgenome")){
205
-    stop("Something went wrong.")
208
+    stop("")
206 209
   }
207 210
   # norm sequences input
208 211
   if(is(sequences,"FaFile")){
209
-    seqnames <- names(Rsamtools::scanFa(sequences))
212
+    seq_seqnames <- names(Rsamtools::scanFa(sequences))
210 213
   } else {
211
-    seqnames <- BSgenome::seqnames(sequences)
214
+    seq_seqnames <- BSgenome::seqnames(sequences)
212 215
   }
213
-  seqnames <- seqnames[seqnames %in% GenomeInfoDb::seqlevels(annotation)]
214
-  seqnames <- seqnames[seqnames %in% GenomeInfoDb::seqnames(seqinfo)]
216
+  seq_seqnames <- 
217
+    seq_seqnames[seq_seqnames %in% GenomeInfoDb::seqlevels(annotation)]
218
+  seq_seqnames <- 
219
+    seq_seqnames[seq_seqnames %in% GenomeInfoDb::seqnames(seqinfo)]
215 220
   if( length(seqnames) == 0L ) {
216 221
     stop("No intersection between chromosome names in fasta, ",
217 222
          "annotation and seqinfo data.", 
... ...
@@ -31,9 +31,9 @@ NULL
31 31
 #' @importFrom Rsamtools idxstatsBam
32 32
 # Extracts sequence names aka. chromosome identifier from list of bam files
33 33
 .get_acceptable_chrom_ident <- function(bamFiles){
34
-  seqnames <- lapply(bamFiles, function(file){
34
+  bf_seqnames <- lapply(bamFiles, function(file){
35 35
     res <- Rsamtools::idxstatsBam(file)
36 36
     return(as.character(res$seqnames))
37 37
   })
38
-  return(unique(unlist(seqnames)))
38
+  return(unique(unlist(bf_seqnames)))
39 39
 }
... ...
@@ -42,10 +42,10 @@ NULL
42 42
 # seqlengths related functions
43 43
 .rebase_GRanges <- function(gr){
44 44
   usn <- .get_unique_seqnames(gr)
45
-  seqnames <- Rle(factor(GenomicRanges::seqnames(gr), levels = usn))
45
+  gr_seqnames <- Rle(factor(GenomicRanges::seqnames(gr), levels = usn))
46 46
   seqlengths <- GenomeInfoDb::seqlengths(gr)[usn]
47 47
   seqinfo <- GenomeInfoDb::Seqinfo(usn, seqlengths)
48
-  GenomicRanges::GRanges(seqnames = seqnames,
48
+  GenomicRanges::GRanges(seqnames = gr_seqnames,
49 49
                          ranges = IRanges::ranges(gr),
50 50
                          strand = BiocGenerics::strand(gr),
51 51
                          seqinfo = seqinfo,
... ...
@@ -75,27 +75,25 @@ NULL
75 75
 # per positions of each element
76 76
 
77 77
 .seqnames_rl <- function(rl){
78
-  seqnames <- as.character(seqnames(rl@unlistData))
78
+  ul_seqnames <- as.character(seqnames(rl@unlistData))
79 79
   width <- as.integer(width(rl@unlistData))
80
-  seqnames <- mapply(rep,seqnames,width,SIMPLIFY = FALSE)
81
-  seqnames <- IRanges::CharacterList(lapply(mapply(seq.int,
80
+  ul_seqnames <- Map(rep,ul_seqnames,width)
81
+  ul_seqnames <- IRanges::CharacterList(lapply(Map(seq.int,
82 82
                                                    start(rl@partitioning),
83
-                                                   end(rl@partitioning),
84
-                                                   SIMPLIFY = FALSE),
85
-                                            function(i){
86
-                                              unname(unlist(seqnames[i]))
87
-                                            }))
88
-  seqnames
83
+                                                   end(rl@partitioning)),
84
+                                               function(i){
85
+                                                 unname(unlist(ul_seqnames[i]))
86
+                                               }))
87
+  ul_seqnames
89 88
 }
90 89
 
91 90
 .strands_rl <- function(rl){
92 91
   strands <- as.character(strand(rl@unlistData))
93 92
   width <- as.integer(width(rl@unlistData))
94
-  strands <- mapply(rep,strands,width,SIMPLIFY = FALSE)
95
-  strands <- IRanges::CharacterList(lapply(mapply(seq.int,
96
-                                                  start(rl@partitioning),
97
-                                                  end(rl@partitioning),
98
-                                                  SIMPLIFY = FALSE),
93
+  strands <- Map(rep,strands,width)
94
+  strands <- IRanges::CharacterList(lapply(Map(seq.int,
95
+                                               start(rl@partitioning),
96
+                                               end(rl@partitioning)),
99 97
                                            function(i){
100 98
                                              unname(unlist(strands[i]))
101 99
                                            }))
... ...
@@ -152,13 +150,12 @@ NULL
152 150
     from <- tmp
153 151
     rm(tmp)
154 152
   }
155
-  ans <- mapply(
153
+  ans <- Map(
156 154
     function(f,t){
157 155
       seq.int(f,t,by)
158 156
     },
159 157
     from,
160
-    to,
161
-    SIMPLIFY = FALSE)
158
+    to)
162 159
   ans <- IRanges::IntegerList(ans)
163 160
   width_x <- IRanges::IntegerList(split(width(ans@partitioning),
164 161
                                         names(ans@partitioning)))
... ...
@@ -201,7 +198,7 @@ NULL
201 198
 .subset_to_condition <- function(conditions, condition){
202 199
   if(condition != "both"){
203 200
     f <- conditions == condition
204
-    if(all(f == FALSE)){
201
+    if(all(!f)){
205 202
       stop("No data for condition '",condition,"' found.")
206 203
     }
207 204
   } else {
... ...
@@ -63,7 +63,7 @@ EndSequenceData(bamfiles, annotation, sequences, seqinfo, ...)
63 63
 \item{condition}{For \code{\link{aggregate}}: condition for which the data
64 64
 should be aggregated.}
65 65
 
66
-\item{name}{For \code{\link[=visualizeDataByCoord]{getDataTrack}}: a valid
66
+\item{name}{For \code{\link[=plotDataByCoord]{getDataTrack}}: a valid
67 67
 transcript name. Must be a name of \code{ranges(x).}}
68 68
 }
69 69
 \value{
... ...
@@ -8,10 +8,10 @@
8 8
 \alias{aggregateData,ModInosine-method}
9 9
 \alias{findMod,ModInosine-method}
10 10
 \alias{getDataTrack,ModInosine-method}
11
-\alias{visualizeDataByCoord,ModInosine,GRanges-method}
12
-\alias{visualizeData,ModInosine-method}
13
-\alias{visualizeDataByCoord,ModSetInosine,GRanges-method}
14
-\alias{visualizeData,ModSetInosine-method}
11
+\alias{plotDataByCoord,ModInosine,GRanges-method}
12
+\alias{plotData,ModInosine-method}
13
+\alias{plotDataByCoord,ModSetInosine,GRanges-method}
14
+\alias{plotData,ModSetInosine-method}
15 15
 \title{Functions for ModInosine}
16 16
 \usage{
17 17
 \S4method{settings}{ModInosine}(x) <- value
... ...
@@ -22,16 +22,16 @@
22 22
 
23 23
 \S4method{getDataTrack}{ModInosine}(x, name, type, ...)
24 24
 
25
-\S4method{visualizeDataByCoord}{ModInosine,GRanges}(x, coord,
26
-  type = "score", window.size = 15L, ...)
25
+\S4method{plotDataByCoord}{ModInosine,GRanges}(x, coord, type = "score",
26
+  window.size = 15L, ...)
27 27
 
28
-\S4method{visualizeData}{ModInosine}(x, name, from = 1L, to = 30L,
28
+\S4method{plotData}{ModInosine}(x, name, from = 1L, to = 30L,
29 29
   type = "score", ...)
30 30
 
31
-\S4method{visualizeDataByCoord}{ModSetInosine,GRanges}(x, coord,
31
+\S4method{plotDataByCoord}{ModSetInosine,GRanges}(x, coord,
32 32
   type = "score&