cex.legend to plotTargetAnnotation, faster ScoreMatrixBin, BigWig ext ScoreMatrix(Bin)

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: genomation
 Type: Package
 Title: Summary, annotation and visualization of genomic data
-Version: 1.1.12
+Version: 1.1.13
 Author: Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Liz Ing-Simmons [ctb]	
 Maintainer: Altuna Akalin <aakalin@gmail.com>, Vedran Franke <vedran.franke@gmail.com>
 Description: A package for summary and annotation of genomic intervals. Users can visualize and 

NEWS

@@ -1,3 +1,12 @@
+genomation 1.1.13
+--------------
+
+IMPROVEMENTS AND BUG FIXES
+
+* add new argument cex.legend to plotTargetAnnotation() to specify the size of the legend.
+* changed ScoreMatrixBin() to run faster when noCovNA=TRUE
+* check not only for .bw but also .bigWig and .bigwig extensions of BigWig file in ScoreMatrix() and ScoreMatrixBin()
+
 genomation 1.1.12
 --------------
 

R/readAnnotate.R

@@ -957,11 +957,10 @@ setMethod("getAssociationWithTSS",
 #'        This option is only valid when x is a 
 #'        \code{AnnotationByGeneParts} object
 #' @param col a vector of colors for piechart or the bar plot
+#' @param cex.legend a numeric value of length 1 to specify the size of the legend. By default 1.
 #' @param ... graphical parameters to be passed to \code{pie} 
 #'            or \code{barplot} functions
 #'
-#' @usage  plotTargetAnnotation(x,precedence=TRUE,col,...)
-#'
 #'
 #' @examples
 #' data(cage)
@@ -981,15 +980,16 @@ setMethod("getAssociationWithTSS",
 setGeneric("plotTargetAnnotation", 
               function(x,
                        precedence=TRUE,
-                       col=getColors(length(x@annotation)),...) 
+                       col=getColors(length(x@annotation)),
+                       cex.legend=1,...) 
                        standardGeneric("plotTargetAnnotation"))
 
 #' @rdname plotTargetAnnotation-methods
 #' @docType methods
 #' @aliases plotTargetAnnotation,AnnotationByFeature-method
 setMethod("plotTargetAnnotation", 
             signature(x = "AnnotationByFeature"),
-            function(x,precedence,col,...){
+            function(x,precedence,col,cex.legend,...){
 
                 props=getTargetAnnotationStats(x,precedence)
 
@@ -999,7 +999,7 @@ setMethod("plotTargetAnnotation",
                 names(props)=paste( paste(round(props),"%"),sep=" ")
 
                 pie(props,cex=0.9,col=col,...)
-                legend("topright",legend=slice.names,fill=col )
+                legend("topright",legend=slice.names,fill=col, cex=cex.legend)
 
             }else{
 

R/readData.R

@@ -120,7 +120,7 @@ readGeneric<-function(file, chr=1,start=2,end=3,strand=NULL,meta.cols=NULL,
                       keep.all.metadata=FALSE, zero.based=FALSE, 
                       remove.unusual=FALSE, header=FALSE, 
                       skip=0, sep="\t"){
-    
+
   # reads the bed files
   df=readTableFast(file, header=header, skip=skip, sep=sep)                    
 
@@ -144,12 +144,12 @@ readGeneric<-function(file, chr=1,start=2,end=3,strand=NULL,meta.cols=NULL,
   # removes nonstandard chromosome names
   if(remove.unusual)
     df = df[grep("_", as.character(df$chr),invert=TRUE),]
-
+  
   g = makeGRangesFromDataFrame(
-                          df, 
-                          keep.extra.columns=FALSE, 
-                          starts.in.df.are.0based=zero.based,
-                          ignore.strand=is.null(strand))
+    df, 
+    keep.extra.columns=FALSE, 
+    starts.in.df.are.0based=zero.based,
+    ignore.strand=is.null(strand))
 
   # this names can not be column names in meta-data
   black.names=c("seqnames", "ranges", "strand", "seqlevels", "seqlengths",
@@ -269,7 +269,7 @@ readBed<-function(file,track.line=FALSE,remove.unusual=FALSE,zero.based=TRUE)
 #' @rdname readBroadPeak
 #' @export
 readBroadPeak<-function(file, track.line=FALSE){
-   
+
   g = readGeneric(file,
                   strand=6,
                   meta.cols=list(name=4,
@@ -305,15 +305,15 @@ readBroadPeak<-function(file, track.line=FALSE){
 #' @rdname readNarrowPeak
 #' @export
 readNarrowPeak<-function(file, track.line=FALSE){
-
+  
   g = readGeneric(file,
                   strand=6,
                   meta.cols=list(name=4,
-                                score=5,
-                                signalValue=7,
-                                pvalue=8,
-                                qvalue=9,
-                                peak=10),
+                                 score=5,
+                                 signalValue=7,
+                                 pvalue=8,
+                                 qvalue=9,
+                                 peak=10),
                   header=FALSE,
                   skip=track.line)
   return(g)
@@ -473,7 +473,7 @@ setMethod("readTranscriptFeatures",
 #' 
 #' @examples
 #' # gff.file = system.file('extdata/chr21.refseq.hg19.gtf', package='genomation')
-#' # gff = gffToGRanges(gff.file, split.group=TRUE)
+#' # gff = gffToGRanges(gff.file)
 #' 
 #' 
 #' @docType methods
@@ -492,6 +492,6 @@ gffToGRanges = function(gff.file, filter=NULL, zero.based=FALSE, ensembl=FALSE){
       stop(paste(filter, 'category does not exist in the gff file'))
     gff = gff[grepl(filter, gff$type)]
   }
-    
+
   return(gff)
 }

R/scoreMatrix.R

@@ -376,7 +376,7 @@ setMethod("ScoreMatrix",signature("character","GRanges"),
 
             if(type == 'bam' & !grepl('bam$',target))
               warning('you have set type="bam", but the designated file does not have .bam extension')
-            if(type == 'bigWig' & !(grepl('bw$',target) | grepl('bigWig$',target)))
+            if(type == 'bigWig' & !grepl('bw$|bigWig$|bigwig$',target))
               warning('you have set type="bigWig", but the designated file does not have .bw extension')
 
             if(type == 'bam')

R/scoreMatrixBin.R

@@ -232,9 +232,8 @@ setMethod("ScoreMatrixBin",signature("GRanges","GRanges"),
                   # figure out which ones are real 0 score
                   # which ones has no coverage
                   # put NAs for no coverage bases
-                  target.rle= endoapply( target.rle,function(x){ x=x-1 
-                                                        x[x<0]=NA
-                                                        x})
+                  runValue(target.rle)=runValue(target.rle)-1
+                  runValue(target.rle)[runValue(target.rle)<0]=NA
 
               }else{
                 # get coverage with weights
@@ -270,7 +269,7 @@ setMethod("ScoreMatrixBin",signature("character","GRanges"),
 
             if(type == 'bam' & !grepl('bam$',target))
               warning('you have set type="bam", but the designated file does not have .bam extension')
-            if(type == 'bigWig' & !grepl('bw$',target))
+            if(type == 'bigWig' & !grepl('bw$|bigWig$|bigwig$',target))
               warning('you have set type="bigWig", but the designated file does not have .bw extension')
 
             if(type == 'bam')

man/gffToGRanges.Rd

@@ -6,24 +6,14 @@
 \title{Converts a gff formated data.frame into a GenomicRanges object.
 The GenomicRanges object needs to be properly formated for the function to work.}
 \usage{
-gffToGRanges(gff.file, track.line = FALSE, split.group = FALSE,
-  split.char = ";", filter = NULL, zero.based = FALSE, ensembl = FALSE)
+gffToGRanges(gff.file, filter = NULL, zero.based = FALSE, ensembl = FALSE)
 }
 \arguments{
 \item{gff.file}{path to a gff formatted file.
 The file can end in \code{.gz}, \code{.bz2}, \code{.xz}, or \code{.zip}
 and/or start with \code{http://} or \code{ftp://}. If the file is not compressed
 it can also start with \code{https://} or \code{ftps://}.}
 
-\item{track.line}{Can be an integer specifying the number of track lines to skip,
-"auto" to detect the header lines automatically
- or FALSE(default) if the bed file doesn't have track lines.
- "auto" detects both UCSC header lines and lines starting with #}
-
-\item{split.group}{boolean, whether to split the 9th column of the file}
-
-\item{split.char}{character that is used as a separator of the 9th column. ';' by default}
-
 \item{filter}{a character designating which elements to retain from the gff file (e.g. exon, CDS, ...)}
 
 \item{zero.based}{\code{boolean} whether the coordinates are 0 or 1 based. 0 is the default}
@@ -39,6 +29,6 @@ The GenomicRanges object needs to be properly formated for the function to work.
 }
 \examples{
 # gff.file = system.file('extdata/chr21.refseq.hg19.gtf', package='genomation')
-# gff = gffToGRanges(gff.file, split.group=TRUE)
+# gff = gffToGRanges(gff.file)
 }
 

man/plotTargetAnnotation-methods.Rd

@@ -6,10 +6,11 @@
 \alias{plotTargetAnnotation,AnnotationByFeature-method}
 \title{Plot annotation categories from AnnotationByGeneParts or AnnotationByFeature}
 \usage{
-plotTargetAnnotation(x,precedence=TRUE,col,...)
+plotTargetAnnotation(x, precedence = TRUE,
+  col = getColors(length(x@annotation)), cex.legend = 1, ...)
 
 \S4method{plotTargetAnnotation}{AnnotationByFeature}(x, precedence = TRUE,
-  col = getColors(length(x@annotation)), ...)
+  col = getColors(length(x@annotation)), cex.legend = 1, ...)
 }
 \arguments{
 \item{x}{a \code{AnnotationByFeature} or
@@ -23,6 +24,8 @@ This option is only valid when x is a
 
 \item{col}{a vector of colors for piechart or the bar plot}
 
+\item{cex.legend}{a numeric value of length 1 to specify the size of the legend. By default 1.}
+
 \item{...}{graphical parameters to be passed to \code{pie}
            or \code{barplot} functions}
 }