DESCRIPTION

@@ -1,29 +1,37 @@
 Package: DiffLogo
 Type: Package
 Title: DiffLogo: A comparative visualisation of biooligomer motifs
-Version: 0.99.2
+Version: 2.13.1
 Date: 2015-02-12
-Author: c( person("Martin", "Nettling", role = c("aut", "cre"), email =
-    "martin.nettling@informatik.uni-halle.de"), person("Hendrik", "Treutler,
-    role = c("aut", "cre"),email="hendrik.treutler@ipb-halle.de"),
-    person("Jan", "Grau", role = c("aut", "ctb"),email=""), person("Jens",
-    "Keilwagen", role = c("aut", "ctb"),email=""), person("Stefan", "Posch",
-    role = "aut")) person("Ivo", "Grosse", role = "aut") )
+Author: c( 
+    person("Martin", "Nettling", role = c("aut", "cre"), email = "martin.nettling@informatik.uni-halle.de"), 
+    person("Hendrik", "Treutler", role = c("aut", "cre"), email = "hendrik.treutler@ipb-halle.de"),
+    person("Jan", "Grau", role = c("aut", "ctb"), email = "grau@informatik.uni-halle.de"), 
+    person("Andrey", "Lando", role = c("aut", "ctb"), email = "dronte@autosome.ru"), 
+    person("Jens", "Keilwagen", role = c("aut", "ctb"), email = "jens.keilwagen@julius-kuehn.de"), 
+    person("Stefan", "Posch", role = "aut", email = "posch@informatik.uni-halle.de"), 
+    person("Ivo", "Grosse", role = "aut", email = "grosse@informatik.uni-halle.de"))
 Depends:
-    R (>= 1.8.0),
+    R (>= 3.4),
     stats,
     cba
+Imports:
+    grDevices, 
+    graphics, 
+    utils, 
+    tools
 Suggests:
     knitr,
-    testthat
-VignetteBuilder: knitr
-Maintainer: Martin Nettling<martin.nettling@informatik.uni-halle.de>
+    testthat,
+    seqLogo,
+    MotifDb
+Maintainer: Hendrik Treutler<hendrik.treutler@gmail.com>
 Description: DiffLogo is an easy-to-use tool to visualize motif differences.
 License: GPL (>= 2)
 URL: https://github.com/mgledi/DiffLogo/
 BugReports: https://github.com/mgledi/DiffLogo/issues
 biocViews: Software, SequenceMatching, MultipleComparison, MotifAnnotation,
-    Visualization
+    Visualization, Alignment
 Collate:
     'alphabet.R'
     'baseDistrs.R'
@@ -32,3 +40,6 @@ Collate:
     'seqLogo.R'
     'stackHeights.R'
     'utilities.R'
+    'diffSeqLogoSupport.R'
+    'pwmAlignment.R'
+RoxygenNote: 6.1.1

NAMESPACE

@@ -1,17 +1,40 @@
+# Generated by roxygen2: do not edit by hand
+
 export(ASN)
 export(Alphabet)
 export(DNA)
+export(FULL_ALPHABET)
 export(RNA)
+export(calculatePvalue)
 export(createDiffLogoObject)
 export(diffLogo)
 export(diffLogoFromPwm)
 export(diffLogoTable)
+export(diffLogoTableConfiguration)
 export(differenceOfICs)
+export(drawDiffLogoTable)
+export(enrichDiffLogoObjectWithPvalues)
+export(enrichDiffLogoTableWithPvalues)
+export(extendPwmsFromAlignmentVector)
+export(getAlphabetFromCharacters)
+export(getAlphabetFromSequences)
 export(getPwmFromAlignment)
+export(getPwmFromAlignmentFile)
+export(getPwmFromFastaFile)
+export(getPwmFromFile)
+export(getPwmFromHomerFile)
+export(getPwmFromPfmOrJasparFile)
+export(getPwmFromPwmFile)
+export(getSequencesFromAlignmentFile)
+export(getSequencesFromFastaFile)
 export(informationContent)
 export(lossOfAbsICDifferences)
+export(multipleLocalPwmsAlignment)
+export(normalizePWM)
 export(normalizedDifferenceOfProbabilities)
+export(prepareDiffLogoTable)
 export(probabilities)
+export(pwmDivergence)
 export(seqLogo)
 export(shannonDivergence)
 export(sumOfAbsICDifferences)
@@ -20,3 +43,21 @@ export(sumProbabilities)
 exportClasses(Alphabet)
 exportClasses(DiffLogo)
 importFrom(cba,order.optimal)
+importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,rgb)
+importFrom(graphics,abline)
+importFrom(graphics,axis)
+importFrom(graphics,legend)
+importFrom(graphics,lines)
+importFrom(graphics,par)
+importFrom(graphics,plot)
+importFrom(graphics,plot.new)
+importFrom(graphics,polygon)
+importFrom(graphics,rect)
+importFrom(graphics,text)
+importFrom(stats,dgamma)
+importFrom(stats,dist)
+importFrom(stats,hclust)
+importFrom(stats,var)
+importFrom(utils,modifyList)
+importFrom(utils,read.delim)

R/alphabet.R

@@ -15,15 +15,16 @@ Letter = function(x,y) {
 ##' @title built alphabet
 ##' @param chars set of symbols
 ##' @param cols set of colors; one for each symbol
+##' @param supportReverseComplement boolean whether the alphabet supports reverse complementation (like DNA/RNA) or not (like ASN)
 ##' @return the Alphabet object
 ##' @export
 ##' @exportClass Alphabet
 ##' @author Martin Nettling
 ##' @examples
-##' DNA = Alphabet(c("A","C","G","T"),c("green4","blue","orange","red"))
-Alphabet = function(chars,cols) {
-   obj = list(chars=chars,cols=cols,size=length(chars))
-   class(obj)="Alphabet"
+##' DNA = Alphabet(c("A","C","G","T"),c("green4","blue","orange","red"),TRUE)
+Alphabet = function(chars, cols, supportReverseComplement) {
+   obj = list(chars=chars,cols=cols,size=length(chars),supportReverseComplement = supportReverseComplement);
+   class(obj)="Alphabet";
    return(obj);
 }
 
@@ -221,21 +222,26 @@ if(FALSE){
 ##' @title DNA alphabet
 ##' @export
 ##' @author Martin Nettling
-##' @examples
-##' motif_folder= "extdata/pwm"
-##' motif_name = "HepG2"
-##' fileName = paste(motif_folder,"/",motif_name,".txt",sep="")
-##' file = system.file(fileName, package = "DiffLogo")
-##' motif = as.matrix(read.delim(file,header=FALSE))
-##' seqLogo(pwm = motif, alphabet=DNA)
-DNA = Alphabet(c("A","C","G","T"),c("green4","blue","orange","red"));
+##' @examples 
+##' DNA
+DNA = Alphabet(
+    c("A","C","G","T"),
+    c("green4","blue","orange","red"),
+    TRUE
+);
 
 ##' the RNA alphabet, i.e. A, C, G, U
 ##'
 ##' @title RNA alphabet
 ##' @export
 ##' @author Martin Nettling
-RNA = Alphabet(c("A","C","G","U"),c("green4","blue","orange","red"));
+##' @examples 
+##' RNA
+RNA = Alphabet(
+    c("A","C","G","U"),
+    c("green4","blue","orange","red"),
+    TRUE
+);
 
 c1="Light green"; c2="Green"; c3="Dark green"; c4="Blue"; c5="violet"; c6="DarkBlue"; c7="Orange"; c8="Pink"; c9="Red";
 
@@ -244,14 +250,23 @@ c1="Light green"; c2="Green"; c3="Dark green"; c4="Blue"; c5="violet"; c6="DarkB
 ##' @title ASN alphabet
 ##' @export
 ##' @author Martin Nettling
-##' @examples
-##' motif_folder= "extdata/alignments"
-##' motif_name = "calamodulin_1"
-##' fileName = paste(motif_folder,"/",motif_name,".txt",sep="")
-##' file = system.file(fileName, package = "DiffLogo")
-##' motif = getPwmFromAlignment(readLines(file), ASN, 1)
-##' seqLogo(pwm = motif, alphabet=ASN)
+##' @examples 
+##' ASN
 ASN = Alphabet(
     c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"),
-    c(c1, c2 ,c3, c3, c5, c1, c6, c4, c7, c4, c4, c3, c8, c3, c7, c9, c9, c4, c5, c5)
-)
+    c(c1, c2 ,c3, c3, c5, c1, c6, c4, c7, c4, c4, c3, c8, c3, c7, c9, c9, c4, c5, c5),
+    FALSE
+);
+
+##' the alphabet of all 26 characters
+##'
+##' @title Complete character alphabet
+##' @export
+##' @author Hendrik Treutler
+##' @examples 
+##' FULL_ALPHABET
+FULL_ALPHABET = Alphabet(
+    c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z"),
+    c(c1, c2 ,c3, c4, c5, c6, c7, c8, c1, c2, c3, c4, c5, c6, c7, c8, c1, c2, c3, c4, c5, c6, c7, c8, c1, c2),
+    FALSE
+);

R/baseDistrs.R

@@ -12,9 +12,9 @@
 ##' motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
 ##' motifs = list()
 ##' for (name in motif_names) {
-##'   fileName = paste(motif_folder,"/",name,".txt",sep="")
+##'   fileName = paste(motif_folder,"/",name,".pwm",sep="")
 ##'   file = system.file(fileName, package = "DiffLogo")
-##'   motifs[[name]] = as.matrix(read.delim(file,header=FALSE))
+##'   motifs[[name]] = getPwmFromPwmFile(file)
 ##' }
 ##' 
 ##' pwm1 = motifs[[motif_names[[1]]]]
@@ -43,9 +43,9 @@ normalizedDifferenceOfProbabilities = function(p1,p2) {
 ##' motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
 ##' motifs = list()
 ##' for (name in motif_names) {
-##'   fileName = paste(motif_folder,"/",name,".txt",sep="")
+##'   fileName = paste(motif_folder,"/",name,".pwm",sep="")
 ##'   file = system.file(fileName, package = "DiffLogo")
-##'   motifs[[name]] = as.matrix(read.delim(file,header=FALSE))
+##'   motifs[[name]] = getPwmFromPwmFile(file)
 ##' }
 ##' 
 ##' pwm1 = motifs[[motif_names[[1]]]]
@@ -75,9 +75,9 @@ differenceOfICs = function(p1,p2) {
 ##' @examples
 ##' motif_folder= "extdata/pwm"
 ##' motif_name = "HepG2"
-##' fileName = paste(motif_folder,"/",motif_name,".txt",sep="")
+##' fileName = paste(motif_folder,"/",motif_name,".pwm",sep="")
 ##' file = system.file(fileName, package = "DiffLogo")
-##' motif = as.matrix(read.delim(file,header=FALSE))
+##' motif = getPwmFromPwmFile(file)
 ##' seqLogo(pwm = motif, baseDistribution = probabilities)
 probabilities = function(p) {
   return(p);