added paper figure to vignette. changed figure widths in vignette. made everythgin compliant (file sizes, ASCII char, etc)

Author: dphansti

.Rbuildignore

@@ -1,2 +1,12 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+.Rproj.user
+.Rhistory
+.RData
+.DS_Store
+inst/doc/Sushi-0*.pdf
+inst/doc/Sushi.log
+inst/doc/Sushi.synctex.gz
+inst/doc/Sushi-concordance.tex
+inst/doc/Sushi.tex
+inst/doc/Sushi.toc

PaperFigure.R

@@ -362,10 +362,8 @@ chromend2         = 73100000
 zoomregion       = c(72998000,73020000)
 chrom2_biomart   = 15
 
-Sushi_transcripts.bed[,1] = paste("chr",Sushi_transcripts.bed[,1],sep="")
-
 # plot transcripts
-pg = plotgenes(Sushi_transcripts.bed,chrom2,chromstart2,chromend2 ,types = Sushi_transcripts.bed$type,
+pg = plotGenes(Sushi_transcripts.bed,chrom2,chromstart2,chromend2 ,types = Sushi_transcripts.bed$type,
                colorby=log10(Sushi_transcripts.bed$score+0.001),colorbycol= SushiColors(5) ,labeltext=FALSE,
                maxrows=50,height=0.4,plotgenetype="box")
 
@@ -492,7 +490,7 @@ chromstart       = 72998000
 chromend         = 73020000
 
 # plot gene structures
-plotgenes(Sushi_genes.bed,chrom_biomart,chromstart,chromend ,types=Sushi_genes.bed$type,
+plotGenes(Sushi_genes.bed,chrom,chromstart,chromend ,
           maxrows=1,bheight=0.2,plotgenetype="arrow",bentline=FALSE,
           labeloffset=1,fontsize=1.2)
 

R/datasetsinfo.R

@@ -5,7 +5,7 @@
 #' @docType data
 #' @usage Sushi_5C.bedpe
 #' @format bedpe format
-#' @source Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012).
+#' @source Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109-113 (2012).
 NULL
 
 #' @name Sushi_ChIAPET_pol2.bedpe
@@ -15,7 +15,7 @@ NULL
 #' @docType data
 #' @usage Sushi_ChIAPET_pol2.bedpe
 #' @format bedpe format
-#' @source Li, G. et al. Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell 148, 84–98 (2012).
+#' @source Li, G. et al. Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell 148, 84-98 (2012).
 NULL
 
 #' @name Sushi_ChIPSeq_CTCF.bedgraph
@@ -25,7 +25,7 @@ NULL
 #' @docType data
 #' @usage Sushi_ChIPSeq_CTCF.bedgraph
 #' @format bedgraph format
-#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
+#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
 NULL
 
 #' @name Sushi_ChIPExo_CTCF.bedgraph
@@ -45,7 +45,7 @@ NULL
 #' @docType data
 #' @usage Sushi_ChIPSeq_pol2.bedgraph
 #' @format bedgraph format
-#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
+#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
 NULL
 
 #' @name Sushi_DNaseI.bedgraph
@@ -55,7 +55,7 @@ NULL
 #' @docType data
 #' @usage Sushi_DNaseI.bedgraph
 #' @format bedgraph format
-#' @source Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83–90 (2012).
+#' @source Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83-90 (2012).
 NULL
 
 #' @name Sushi_ChIPSeq_pol2.bed
@@ -65,7 +65,7 @@ NULL
 #' @docType data
 #' @usage Sushi_ChIPSeq_pol2.bed
 #' @format bed format
-#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
+#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
 NULL
 
 
@@ -76,7 +76,7 @@ NULL
 #' @docType data
 #' @usage Sushi_ChIPSeq_severalfactors.bed
 #' @format bed format
-#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
+#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
 NULL
 
 #' @name Sushi_RNASeq_K562.bedgraph
@@ -86,7 +86,7 @@ NULL
 #' @docType data
 #' @usage Sushi_RNASeq_K562.bedgraph
 #' @format bedgraph format
-#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
+#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
 NULL
 
 
@@ -97,7 +97,7 @@ NULL
 #' @docType data
 #' @usage Sushi_RNASeq_K562.bedgraph
 #' @format bedgraph format
-#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
+#' @source Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
 NULL
 
 #' @name Sushi_GWAS.bed
@@ -107,7 +107,7 @@ NULL
 #' @docType data
 #' @usage Sushi_GWAS.bed
 #' @format bed format
-#' @source Ehret, G. B. et al. Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature 478, 103–109 (2011).
+#' @source Ehret, G. B. et al. Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature 478, 103-109 (2011).
 NULL
 
 #' @name Sushi_HiC.matrix
@@ -137,7 +137,7 @@ NULL
 #' @docType data
 #' @usage Sushi_transcripts.bed
 #' @format bed format
-#' @source http://www.biomart.org/ and Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
+#' @source http://www.biomart.org/ and Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
 NULL
 
 #' @name Sushi_hg18_genome
@@ -146,7 +146,7 @@ NULL
 #' @docType data
 #' @usage Sushi_hg18_genome
 #' @format two columns (column 1 = chromosome name, column 2 = length of chromosome)
-#' @source http://www.biomart.org/ and Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
+#' @source http://www.biomart.org/ and Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
 NULL
 
 

R/labelplot.R

@@ -12,6 +12,8 @@
 #' @param titlecex cex of title See \code{\link{par}}
 #' @param letterline line of letter. See \code{\link{par}}
 #' @param titleline line of title See \code{\link{par}}
+#' @param lettercol color of letter. See \code{\link{par}}
+#' @param titlecol color of title See \code{\link{par}}
 #' @export
 #' @examples
 #' 

R/opaque.R

@@ -12,7 +12,7 @@ opaque <- function(color=SushiColors(7)(7),transparency=0.5)
   if (length(color) == 1)
   {
     colrgb = col2rgb(color)
-    newcol = rgb(colrgb[1],colrgb[2],colrgb[3],alpha=transparency * 255,max = 255)
+    newcol = rgb(colrgb[1],colrgb[2],colrgb[3],alpha=transparency * 255,maxColorValue = 255)
     return(newcol)
   }
   else
@@ -21,7 +21,7 @@ opaque <- function(color=SushiColors(7)(7),transparency=0.5)
     for (col in color)
     {
       colrgb = col2rgb(col)
-      newcols = c(newcols,rgb(colrgb[1],colrgb[2],colrgb[3],alpha=transparency * 255,max = 255))
+      newcols = c(newcols,rgb(colrgb[1],colrgb[2],colrgb[3],alpha=transparency * 255,maxColorValue = 255))
     }
     return (newcols)
   }

R/plotgenes.R

@@ -34,13 +34,13 @@
 #' chromend         = 73020000
 #' chrom_biomart    = 15
 #' 
-#' plotgenes(Sushi_genes.bed,chrom_biomart,chromstart,chromend ,types=Sushi_genes.bed$type,
+#' plotGenes(Sushi_genes.bed,chrom_biomart,chromstart,chromend ,types=Sushi_genes.bed$type,
 #'      maxrows=1,height=0.5,plotgenetype="arrow",bentline=FALSE,col="blue",
 #'      labeloffset=1,fontsize=1.2)
 #' 
 #' labelgenome( chrom, chromstart,chromend,side=1,scipen=20,n=3,scale="Mb",line=.18,chromline=.5,scaleline=0.5)
 #'
-plotgenes <-
+plotGenes <-
 function(transcripts, chrom=NULL, chromstart=NULL,chromend=NULL,
                       col=SushiColors(2)(2)[1],bheight=0.3,lheight=0.3,bentline=TRUE,
                       packrow=TRUE,maxrows=10000,
@@ -370,6 +370,11 @@ function(transcripts, chrom=NULL, chromstart=NULL,chromend=NULL,
 
   # filter out rows above max row 
   transcriptinfo = transcriptinfo[which(is.na(transcriptinfo$plotrow)==FALSE),]
+  
+  # filter out transcrits that don't overlap region
+  transcriptinfo = transcriptinfo[which((transcriptinfo[,2] > chromstart & transcriptinfo[,2] < chromend)
+                       | (transcriptinfo[,3] > chromstart & transcriptinfo[,3] < chromend)),]
+   
 
   plot(c(1,1),xlim=c(chromstart,chromend),ylim=c(0.5,( max(transcriptinfo$plotrow) + offsettop)),type ='n',bty='n',xaxt='n',yaxt='n',ylab="",xlab="",xaxs="i")
 

Sushi.Rproj

@@ -14,4 +14,5 @@ LaTeX: pdfLaTeX
 
 BuildType: Package
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageBuildArgs: --resave-data
 PackageRoxygenize: rd

Sushi.bib

@@ -0,0 +1,92 @@
+@article{encode_integrated_2012,
+  title = {An integrated encyclopedia of {DNA} elements in the human genome},
+  author = {{The ENCODE Project Consortium}},
+  journal = {Nature},
+  year = {2012},
+  volume = {489},
+  issn = {1476-4687},
+  url = {http://www.ncbi.nlm.nih.gov/pubmed/22955616},
+  doi = {10.1038/nature11247},
+  number = {7414},
+  month = sep,
+  note = {{PMID:} 22955616},
+  pages = {57--74},
+}
+@article{fiveC,
+  title = {The long-range interaction landscape of gene promoters},
+  volume = {489},
+  doi = {10.1038/nature11279},
+  number = {7414},
+  journal = {Nature},
+  author = {A Sanyal and BR Lajoie and G Jain and J Dekker},
+  month = sep,
+  year = {2012},
+  note = {{PMID:} 22955621},
+  pages = {109--113},
+}
+@article{chiapet,
+  title = {Extensive promoter-centered chromatin interactions provide a
+topological basis for transcription regulation},
+  volume = {148},
+  doi = {10.1016/j.cell.2011.12.014},
+  journal = {Cell},
+  author = {G Li and X Ruan and RK Auerbach and KS Sandhu and M Zheng and P Wang and HM Poh and Y Goh and J Lim and J Zhang and HS Sim and SQ Peh and FH Mulawadi and CT Ong and YL Orlov and S Hong and Z Zhang and S Landt and D Raha and G Euskirchen and CL Wei and W Ge and H Wang and C Davis and KI Fisher-Aylor and A Mortazavi and M Gerstein and T Gingeras and B Wold and Y Sun and MJ Fullwood and E Cheung and E Liu and WK Sung and M Snyder and Y Ruan},
+  month = jan,
+  year = {2012},
+  note = {{PMID:} 22265404},
+  pages = {84--98},
+}
+@article{chipexo,
+  title = {Comprehensive genome-wide protein-DNA interactions detected 
+at single-nucleotide resolution},
+  volume = {147},
+  doi = {10.1016/j.cell.2011.11.013},
+  journal = {Cell},
+  author = {HS Rhee and BF Pugh},
+  month = dec,
+  year = {2011},
+  note = {{PMID:} 22153082},
+}
+
+@article{dnaseI,
+  title = {An expansive human regulatory lexicon encoded in transcription factor footprints},
+  volume = {489},
+  doi = {10.1038/nature11212},
+  journal = {Nature},
+  author = {S Neph S and J Vierstra and AB Stergachis and AP Reynolds and E Haugen and B Vernot and RE Thurman
+and S John and R Sandstrom and AK Johnson and MT Maurano and R Humbert and E Rynes and H Wang and S Vong
+and K Lee and D Bates and M Diegel and V Roach and D Dunn and J Neri and A Schafer and RS Hansen and T 
+Kutyavin and E Giste and M Weaver and T Canfield and P Sabo and M Zhang and G Balasundaram and R Byron
+and MJ MacCoss and JM Akey and MA Bender and M Groudine and R Kaul and JA Stamatoyannopoulos},
+  month = sep,
+  year = {2012},
+  pages = {83-90},
+  note = {{PMID:} 22955618},
+}
+
+@article{GWAS,
+  title = {Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk},
+  volume = {478},
+  doi = {10.1038/nature10405},
+  journal = {Nature},
+  author = {{International Consortium for Blood Pressure Genome-Wide Association Studies}},
+  month = sep,
+  year = {2011},
+  note = {{PMID:} 21909115},
+}
+
+@article{HiC,
+  title = {Topological domains in mammalian genomes identified by analysis of chromatin
+interactions},
+  volume = {485},
+  doi = {10.1038/nature11082},
+  journal = {Nature},
+  author = {JR Dixon and S Selvaraj and F Yue and A Kim and Y Li and Y Shen and M Hu and JS Liu and B Ren},
+  month = sep,
+  year = {2012},
+  note = {{PMID:} 22495300},
+}
+@online{biomart,
+title = {Biomart},
+url = {http://www.biomart.org/}
+}