@@ -1,7 +1,7 @@

 Package: trackViewer

 Type: Package

 Title: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

-Version: 1.23.0

+Version: 1.23.1

 Author@R: c(person(given="Jianhong", family="Ou", email="jianhong.ou@duke.edu", 

         role=c("aut", "cre"), comment=c(ORCID="0000-0002-8652-2488")), 

         person(given="Julie", family="Zhu", middle="Lihua", 

@@ -11,7 +11,7 @@ Maintainer: Jianhong Ou <jianhong.ou@duke.edu>

 Description: Visualize mapped reads along with annotation as track layers for NGS dataset 

   such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

 License: GPL (>= 2)

-Depends: R (>= 3.1.0), grDevices, methods, GenomicRanges, grid

+Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid

 Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors,

         rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport,

         htmlwidgets, plotrix, Rgraphviz, InteractionSet, graph, utils

@@ -19,5 +19,5 @@ Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db,

         BiocStyle, knitr, VariantAnnotation, httr, htmltools

 biocViews: Visualization

 VignetteBuilder: knitr

-RoxygenNote: 6.1.1

+RoxygenNote: 7.0.2

 Encoding: UTF-8

@@ -11,6 +11,7 @@ export(geneModelFromTxdb)

 export(geneTrack)

 export(getCurTrackViewport)

 export(getLocation)

+export(gi2track)

 export(gieStain)

 export(ideogramPlot)

 export(importBam)

@@ -72,6 +73,8 @@ importFrom(GenomeInfoDb,seqnames)

 importFrom(Gviz,GeneRegionTrack)

 importFrom(Rgraphviz,layoutGraph)

 importFrom(Rgraphviz,renderGraph)

+importFrom(S4Vectors,first)

+importFrom(S4Vectors,second)

 importFrom(grDevices,as.raster)

 importFrom(grDevices,col2rgb)

 importFrom(grDevices,colorRampPalette)

@@ -1,3 +1,7 @@

+Changes in version 1.23.1

+

+    o add interactionData track.

+    

 Changes in version 1.21.18

     o update NEWS file from "CHANGES IN VERSION" to "Changes in version".

@@ -219,7 +219,7 @@ setClass("trackStyle",

 #' the scores of a given track. It should contain score metadata. When dat2

 #' and dat is paired, dat will be drawn as positive value where dat2 will be 

 #' drawn as negative value (-1 * score)

-#' @slot type The type of track. It could be 'data', 'gene', 'transcript' or 'lollipopData'.

+#' @slot type The type of track. It could be 'data', 'gene', 'transcript', 'lollipopData' or 'interactionData'.

 #' @slot format The format of the input. It could be "BED", "bedGraph",

 #' "WIG", "BigWig" or "BAM"

 #' @slot style Object of class \code{\link{trackStyle}}

@@ -242,8 +242,8 @@ setClass("track", representation(dat="GRanges",

                                  style="trackStyle",

                                  name="character"),

          validity=function(object){

-             if(!object@type %in% c("data", "gene", "transcript", "lollipopData"))

-                 return("type must be 'data', 'transcript', 'gene', 'lollipopData'")

+             if(!object@type %in% c("data", "gene", "transcript", "lollipopData", "interactionData"))

+                 return("type must be 'data', 'transcript', 'gene', 'lollipopData', 'interactionData'")

              if(object@type=="data"){

                  if(!object@format %in% c("BED", "bedGraph", "WIG", "BigWig", "BAM"))

                      return("format must be one of \"BED\", 

@@ -276,13 +276,20 @@ setClass("track", representation(dat="GRanges",

                    }

                  }

                }else{

-                 if(is.null(mcols(object@dat)$feature))

-                   return("The metadata of dat must contain colnumn 'feature'") 

-                 if(length(object@dat2)>0){

-                   if(is.null(object@dat2$score))

-                     return("dat2 should contain score metadata.")

-                   if(!all(width(object@dat2)==1)){

-                     return("Width for lollipop data must be 1")

+                 if(object@type=="interactionData"){

+                   if(is.null(object@dat$score))

+                     return("dat should contain score metadata.")

+                   if(length(object@dat2)!=length(object@dat))

+                     return("dat2 should be same length of dat.")

+                 }else{

+                   if(is.null(mcols(object@dat)$feature))

+                     return("The metadata of dat must contain colnumn 'feature'") 

+                   if(length(object@dat2)>0){

+                     if(is.null(object@dat2$score))

+                       return("dat2 should contain score metadata.")

+                     if(!all(width(object@dat2)==1)){

+                       return("Width for lollipop data must be 1")

+                     }

                    }

                  }

                }

new file mode 100644

@@ -0,0 +1,20 @@

+#' convert GInteractions to track object

+#' @description Convert GInteractions object to track object

+#' @param gi an object of GInteractions

+#' @return an track object

+#' @importFrom S4Vectors first second

+#' @export

+#' @examples 

+#' gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds", package="trackViewer"))

+#' gi2track(gi)

+gi2track <- function(gi){

+  stopifnot(is(gi, "GInteractions"))

+  a <- first(gi)

+  if(length(gi$score)==length(a)){

+    a$score <- gi$score

+  }else{

+    a$score <- 1

+  }

+  return(new("track", dat=a, dat2=second(gi),

+             type="interactionData", format="BED"))

+}

\ No newline at end of file

@@ -58,7 +58,7 @@ optimizeStyle <- function(trackList, viewerStyle=trackViewerStyle(), theme=NULL)

         stop("trackList must be an object of \"trackList\"

              (See ?trackList) or a list of track")

     }

-    if(trackList[[length(trackList)]]@type=="data" && viewerStyle@margin[3] < .02)

+    if(trackList[[length(trackList)]]@type %in% c("data", "interactionData") && viewerStyle@margin[3] < .02)

         viewerStyle@margin[3] <- .02

     ##put x-axis?

     dataTracksIdx <- sapply(trackList, function(.ele) .ele@type=="data")

@@ -87,14 +87,14 @@ optimizeStyle <- function(trackList, viewerStyle=trackViewerStyle(), theme=NULL)

     ##put y-axis?

     if(all(!(sapply(trackList, function(.ele) .ele@style@yaxis@label)))){

         for(i in 1:length(trackList)){

-            if(trackList[[i]]@type=="data"){

+            if(trackList[[i]]@type %in% c("data")){

                 trackList[[i]]@style@yaxis@label <- TRUE

                 trackList[[i]]@style@yaxis@gp <- 

                     c(trackList[[i]]@style@yaxis@gp, 

                       cex=optFontSize("y", viewerStyle))

                 trackList[[i]]@style@marginTop <- .1

             }

-          if(trackList[[i]]@type=="lollipopData"){

+          if(trackList[[i]]@type %in% c("lollipopData", "interactionData")){

             trackList[[i]]@style@yaxis@draw <- FALSE

           }

         }

@@ -104,7 +104,7 @@ optimizeStyle <- function(trackList, viewerStyle=trackViewerStyle(), theme=NULL)

     if(!is.null(theme)){

         if(theme=="bw"){

             for(i in 1:length(trackList)){

-                if(trackList[[i]]@type %in% c("data", "lollipopData")){

+                if(trackList[[i]]@type %in% c("data", "lollipopData", "interactionData")){

                     trackList[[i]]@style@ylabpos="bottomleft"

                     trackList[[i]]@style@marginBottom=.2

                     trackList[[i]]@style@ylabgp=

@@ -123,7 +123,7 @@ optimizeStyle <- function(trackList, viewerStyle=trackViewerStyle(), theme=NULL)

         }

         if(theme=="col"){

             for(i in 1:length(trackList)){

-                if(trackList[[i]]@type %in% c("data", "lollipopData")){

+                if(trackList[[i]]@type %in% c("data", "lollipopData", "interactionData")){

                     trackList[[i]]@style@ylabpos="bottomleft"

                     trackList[[i]]@style@marginBottom=.2

                     trackList[[i]]@style@ylabgp=

@@ -145,7 +145,7 @@ optimizeStyle <- function(trackList, viewerStyle=trackViewerStyle(), theme=NULL)

         safeColors <- c("#000000", "#D55E00", "#009E73", "#0072B2",

                         "#56B4E9", "#CC79A7", "#E69F00", "#BEBEBE")

         for(i in 1:length(trackList)){

-          if(trackList[[i]]@type %in% c("data", "lollipopData")){

+          if(trackList[[i]]@type %in% c("data", "lollipopData", "interactionData")){

             trackList[[i]]@style@ylabpos="bottomleft"

             trackList[[i]]@style@marginBottom=.2

             trackList[[i]]@style@ylabgp=

new file mode 100644

@@ -0,0 +1,58 @@

+plotInteractionDataTrack <- function(.dat, .dat2, chr, strand, scale, color, yscale){

+  names(.dat) <- NULL

+  mcols(.dat) <- mcols(.dat)[, "score"]

+  colnames(mcols(.dat)) <- "score"

+  if(missing(yscale)) yscale <- c(0, 1)

+  if(length(.dat)<1){

+    return()

+  }

+  ## plot rect at position

+  ## x = (center1 + center2)/2

+  ## y = unit((x-scale[1]+1)/((scale[2] - scale[1] + 1)/2), "npc")

+  ## width = width(x1)

+  ## height = uint(width(x2)/(scale[2] - scale[1] + 1), "npc")

+  ## rot = 45 degree

+  ## color = colorRampPalette(color)(100)

+  rg <- range(.dat$score[!is.na(.dat$score)])

+  if(length(rg)!=2){

+    return()

+  }

+  breaks <- seq(0, ceiling(rg[2]), length.out = 101)

+  if(length(unique(color))==1){

+    if(!tolower(color[1]) %in% c("white", "#ffffff", "#fff")){

+      color <- c("white", color[1])

+    }else{

+      color <- c("black", color[1])

+    }

+  }

+  if(length(color)==0){

+    color <- c("white", "red")

+  }

+  crp <- colorRampPalette(color)(100)

+  mc <- cut(.dat$score, breaks = breaks, labels = crp)

+  mc <- as.character(mc)

+  inRange <- function(x, scale){

+    x>=scale[1] & x<=scale[2]

+  }

+  ym <- (scale[2]-scale[1] + 1)/2

+  xa <- (end(.dat) + start(.dat2))/2

+  xb <- (start(.dat) + start(.dat2))/2

+  xc <- (start(.dat) + end(.dat2))/2

+  xd <- (end(.dat) + end(.dat2))/2

+  ya <- (xa-end(.dat)+1)/ym

+  yb <- (xb-start(.dat)+1)/ym

+  yc <- (xc-start(.dat)+1)/ym

+  yd <- (xd-end(.dat)+1)/ym

+  irx <- inRange(xa, scale) | inRange(xb, scale) | inRange(xc, scale) | inRange(xd, scale)

+  iry <- inRange(ya, yscale) | inRange(yb, yscale) | inRange(yc, yscale) | inRange(yd, yscale)

+  for(i in seq_along(.dat)){

+    if(irx[i] && iry[i]){

+      grid.polygon(x=c(xa[i], xb[i], xc[i], xd[i]), 

+                   y=unit(c(ya[i], yb[i], yc[i], yd[i]), "npc"), 

+                   default.units="native",

+                   gp = gpar(fill=mc[i], col = NA))

+    }

+  }

+  # legend

+}

+

@@ -145,7 +145,7 @@ plotTrack <- function(name, track, curViewStyle, curYpos,

                           width=1, 

                           just=c(0,0))) ## vp2

     xy <- list()

-    if(track@type %in% c("data", "lollipopData")){

+    if(track@type %in% c("data", "lollipopData", "interactionData")){

         if(track@type=="data") {

           ##plot yaxis

           drawYaxis(yscale, style@yaxis, curViewStyle)

@@ -182,51 +182,68 @@ plotTrack <- function(name, track, curViewStyle, curYpos,

             drawXscale(style@xscale)

           }

         }else{

-          pushViewport(viewport(x=curViewStyle@margin[2], y=0, 

-                                height=1, 

-                                width=1-curViewStyle@margin[2]-curViewStyle@margin[4], 

-                                clip="on",

-                                just=c(0,0), 

-                                xscale=xscale))

-          ybase <- ifelse(length(track@dat2)>0, .5, 0)

-          

-          LINEW <- as.numeric(convertX(unit(1, "line"), "npc"))

-          LINEH <- as.numeric(convertY(unit(1, "line"), "npc"))

-          ## GAP the gaps between any elements

-          GAP <- .2 * LINEH

-          ratio.yx <- 1/as.numeric(convertX(unit(1, "snpc"), "npc"))

-          getMaxHeight <- function(lollipopData){

-            if(length(lollipopData)==0) return(0)

-            TYPES <- c("circle", "pie", "pin", "pie.stack", "flag")

-            type <- if(is.list(lollipopData$type)) lollipopData$type[[1]] else lollipopData$type[1]

-            if(length(type)==0) type <- "circle"

-            if(!type %in% TYPES) type <- "circle"

-            cex <- if(is.list(lollipopData$cex)) lollipopData$cex[[1]] else lollipopData$cex[1]

-            if(length(cex)==0) cex <- 1

-            scoreMax0 <- scoreMax <- 

-              if(length(lollipopData$score)>0) ceiling(max(c(lollipopData$score, 1), na.rm=TRUE)) else 1

-            if(type=="pie.stack") scoreMax <- length(unique(lollipopData$stack.factor))

-            if(!type %in% c("pie", "pie.stack")){

-              if(scoreMax>10) {

-                scoreMax <- 10*scoreMax0/scoreMax

-              }else{

-                scoreMax <- scoreMax0

+          if(track@type=="lollipopData"){

+            pushViewport(viewport(x=curViewStyle@margin[2], y=0, 

+                                  height=1, 

+                                  width=1-curViewStyle@margin[2]-curViewStyle@margin[4], 

+                                  clip="on",

+                                  just=c(0,0), 

+                                  xscale=xscale))

+            ybase <- ifelse(length(track@dat2)>0, .5, 0)

+            

+            LINEW <- as.numeric(convertX(unit(1, "line"), "npc"))

+            LINEH <- as.numeric(convertY(unit(1, "line"), "npc"))

+            ## GAP the gaps between any elements

+            GAP <- .2 * LINEH

+            ratio.yx <- 1/as.numeric(convertX(unit(1, "snpc"), "npc"))

+            getMaxHeight <- function(lollipopData){

+              if(length(lollipopData)==0) return(0)

+              TYPES <- c("circle", "pie", "pin", "pie.stack", "flag")

+              type <- if(is.list(lollipopData$type)) lollipopData$type[[1]] else lollipopData$type[1]

+              if(length(type)==0) type <- "circle"

+              if(!type %in% TYPES) type <- "circle"

+              cex <- if(is.list(lollipopData$cex)) lollipopData$cex[[1]] else lollipopData$cex[1]

+              if(length(cex)==0) cex <- 1

+              scoreMax0 <- scoreMax <- 

+                if(length(lollipopData$score)>0) ceiling(max(c(lollipopData$score, 1), na.rm=TRUE)) else 1

+              if(type=="pie.stack") scoreMax <- length(unique(lollipopData$stack.factor))

+              if(!type %in% c("pie", "pie.stack")){

+                if(scoreMax>10) {

+                  scoreMax <- 10*scoreMax0/scoreMax

+                }else{

+                  scoreMax <- scoreMax0

+                }

               }

+              getHeight(lollipopData, 

+                        ratio.yx, LINEW, GAP, cex, type,

+                        scoreMax=scoreMax,

+                        level="data")

+            }

+            maxHeight <- max(c(getMaxHeight(track@dat), getMaxHeight(track@dat2)), na.rm = TRUE)

+            if(length(track@dat2)>0) maxHeight + .5

+            plotLollipopData(track@dat, xlim, chr, style@yaxis@draw, gpar(),

+                             ybase, side="top", main=style@yaxis@main,

+                             baselineCol=style@color[1], maxHeight=maxHeight)

+            if(length(track@dat2)>0) {

+              plotLollipopData(track@dat2, xlim, chr, style@yaxis@draw, gpar(),

+                               ybase, side="bottom", main=style@yaxis@main,

+                               baselineCol=style@color[2], maxHeight=maxHeight)

+            }

+          }else{##interactionData

+            ##plot yaxis

+            drawYaxis(yscale, style@yaxis, curViewStyle)

+            pushViewport(viewport(x=curViewStyle@margin[2], y=0, 

+                                  height=1, 

+                                  width=1-curViewStyle@margin[2]-curViewStyle@margin[4], 

+                                  clip="on",

+                                  just=c(0,0), 

+                                  xscale=xscale, 

+                                  yscale=yscale))

+            ##grid.clip()

+            ##for dat interaction: dat, dat2, pair.

+            if(length(track@dat)==length(track@dat2)){

+              plotInteractionDataTrack(track@dat, track@dat2, chr, strand, xlim, style@color[1], yscale=yscale)

             }

-            getHeight(lollipopData, 

-                      ratio.yx, LINEW, GAP, cex, type,

-                      scoreMax=scoreMax,

-                      level="data")

-          }

-          maxHeight <- max(c(getMaxHeight(track@dat), getMaxHeight(track@dat2)), na.rm = TRUE)

-          if(length(track@dat2)>0) maxHeight + .5

-          plotLollipopData(track@dat, xlim, chr, style@yaxis@draw, gpar(),

-                           ybase, side="top", main=style@yaxis@main,

-                           baselineCol=style@color[1], maxHeight=maxHeight)

-          if(length(track@dat2)>0) {

-            plotLollipopData(track@dat2, xlim, chr, style@yaxis@draw, gpar(),

-                             ybase, side="bottom", main=style@yaxis@main,

-                             baselineCol=style@color[2], maxHeight=maxHeight)

           }

         }

     }else{##track@type=="transcript" or "gene"

@@ -132,26 +132,44 @@ filterTracks <- function(tl, chrom, from, to, st){

                 }

             }

         }else{

-          if(tl[[i]]@type=="lollipopData"){

+          if(tl[[i]]@type=="interactionData"){## dat, dat2 are paired

             dat <- tl[[i]]@dat

+            dat2 <- tl[[i]]@dat2

+            keep <- ((end(dat)>=from & start(dat)<=to) |

+                       (end(dat2)>=from & start(dat2)<=to)) & 

+              seqnames(dat)==chrom & seqnames(dat2)==chrom

+            ## remove duplicates

+            idx1 <- paste(as.character(seqnames(dat)), start(dat), end(dat),

+                          as.character(seqnames(dat2)), start(dat2), end(dat2))

+            idx2 <- paste(as.character(seqnames(dat2)), start(dat2), end(dat2),

+                          as.character(seqnames(dat)), start(dat), end(dat))

+            idx <- ifelse(start(dat)<start(dat2), idx1, idx2)

+            keep <- keep & (!duplicated(idx))

+            

+            tl[[i]]@dat <- dat[keep]

+            tl[[i]]@dat2 <- dat2[keep]

           }else{

-            dat <- range(tl[[i]]@dat)

-          }

+            if(tl[[i]]@type=="lollipopData"){

+              dat <- tl[[i]]@dat

+            }else{

+              dat <- range(tl[[i]]@dat)

+            }

             dat <- dat[end(dat)>=from &

-                           start(dat)<=to &

-                           seqnames(dat)==chrom]

+                         start(dat)<=to &

+                         seqnames(dat)==chrom]

             dat2 <- tl[[i]]@dat2

             if(length(dat2)>0){

-                dat2 <- dat2[end(dat2)>=from &

-                                 start(dat2)<=to &

-                                 seqnames(dat2)==chrom]

+              dat2 <- dat2[end(dat2)>=from &

+                             start(dat2)<=to &

+                             seqnames(dat2)==chrom]

             }

             if(tl[[i]]@type=="lollipopData"){

               tl[[i]]@dat <- dat

               tl[[i]]@dat2 <- dat2

             }

             if(length(dat)==0 && length(dat2)==0)

-                tl[[i]]@style@height <- 0

+              tl[[i]]@style@height <- 0

+          }

         }

     }

     tl

@@ -173,7 +191,12 @@ getYlim <- function(tl, op){

                 }

                 ylim <- range(c(0, ylim))

             }else{

+              if(.ele@type == "interactionData"){

+                ## max interaction height

+                ylim <- c(0, 1)

+              }else{

                 ylim <- c(0, 0)

+              }

             }            

         }

         ylim

new file mode 100644

Binary files /dev/null and b/inst/extdata/ctcf.sample.rds differ

new file mode 100644

Binary files /dev/null and b/inst/extdata/nij.chr6.51120000.53200000.gi.rds differ

@@ -4,8 +4,13 @@

 \alias{GRoperator}

 \title{GRanges operator}

 \usage{

-GRoperator(A, B, col = "score", operator = c("+", "-", "*", "/", "^",

-  "\%\%"), ignore.strand = TRUE)

+GRoperator(

+  A,

+  B,

+  col = "score",

+  operator = c("+", "-", "*", "/", "^", "\%\%"),

+  ignore.strand = TRUE

+)

 }

 \arguments{

 \item{A}{an object of GRanges}

@@ -4,9 +4,17 @@

 \alias{addArrowMark}

 \title{Add arrow mark to the figure at a given position}

 \usage{

-addArrowMark(pos = grid.locator(), label = NULL, angle = 15,

-  length = unit(0.25, "inches"), col = "red", cex = 1,

-  quadrant = 4, type = "closed", vp = NULL)

+addArrowMark(

+  pos = grid.locator(),

+  label = NULL,

+  angle = 15,

+  length = unit(0.25, "inches"),

+  col = "red",

+  cex = 1,

+  quadrant = 4,

+  type = "closed",

+  vp = NULL

+)

 }

 \arguments{

 \item{pos}{A unit object representing the location of arrow mark to be placed 

@@ -4,8 +4,7 @@

 \alias{addGuideLine}

 \title{Add guide lines to the tracks}

 \usage{

-addGuideLine(guideLine, col = "gray", lty = "dashed", lwd = 1,

-  vp = NULL)

+addGuideLine(guideLine, col = "gray", lty = "dashed", lwd = 1, vp = NULL)

 }

 \arguments{

 \item{guideLine}{The genomic coordinates to draw the lines}

@@ -4,8 +4,14 @@

 \alias{browseTracks}

 \title{browse tracks}

 \usage{

-browseTracks(trackList, gr = GRanges(), ignore.strand = TRUE,

-  width = NULL, height = NULL, ...)

+browseTracks(

+  trackList,

+  gr = GRanges(),

+  ignore.strand = TRUE,

+  width = NULL,

+  height = NULL,

+  ...

+)

 }

 \arguments{

 \item{trackList}{an object of \code{\link{trackList}}}

@@ -4,12 +4,24 @@

 \alias{dandelion.plot}

 \title{dandelion.plots}

 \usage{

-dandelion.plot(SNP.gr, features = NULL, ranges = NULL,

-  type = c("fan", "circle", "pie", "pin"), newpage = TRUE,

-  ylab = TRUE, ylab.gp = gpar(col = "black"), xaxis = TRUE,

-  xaxis.gp = gpar(col = "black"), yaxis = FALSE, yaxis.gp = gpar(col

-  = "black"), legend = NULL, cex = 1, maxgaps = 1/50,

-  heightMethod = NULL, ...)

+dandelion.plot(

+  SNP.gr,

+  features = NULL,

+  ranges = NULL,

+  type = c("fan", "circle", "pie", "pin"),

+  newpage = TRUE,

+  ylab = TRUE,

+  ylab.gp = gpar(col = "black"),

+  xaxis = TRUE,

+  xaxis.gp = gpar(col = "black"),

+  yaxis = FALSE,

+  yaxis.gp = gpar(col = "black"),

+  legend = NULL,

+  cex = 1,

+  maxgaps = 1/50,

+  heightMethod = NULL,

+  ...

+)

 }

 \arguments{

 \item{SNP.gr}{A object of \link[GenomicRanges:GRanges-class]{GRanges} or 

@@ -4,8 +4,16 @@

 \alias{geneModelFromTxdb}

 \title{Prepare gene model from an object of TxDb}

 \usage{

-geneModelFromTxdb(txdb, orgDb, gr, chrom, start, end, strand = c("*",

-  "+", "-"), txdump = NULL)

+geneModelFromTxdb(

+  txdb,

+  orgDb,

+  gr,

+  chrom,

+  start,

+  end,

+  strand = c("*", "+", "-"),

+  txdump = NULL

+)

 }

 \arguments{

 \item{txdb}{An object of \code{\link[GenomicFeatures:TxDb-class]{TxDb}}}

new file mode 100644

@@ -0,0 +1,21 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/gi2track.R

+\name{gi2track}

+\alias{gi2track}

+\title{convert GInteractions to track object}

+\usage{

+gi2track(gi)

+}

+\arguments{

+\item{gi}{an object of GInteractions}

+}

+\value{

+an track object

+}

+\description{

+Convert GInteractions object to track object

+}

+\examples{

+gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds", package="trackViewer"))

+gi2track(gi)

+}

@@ -4,14 +4,20 @@

 \alias{ideogramPlot}

 \title{plot ideogram with data}

 \usage{

-ideogramPlot(ideo, dataList, layout = NULL, horiz = TRUE,

-  parameterList = list(vp = plotViewport(margins = c(0.1, 4.1, 0.3,

-  0.1)), ideoHeight = unit(1/(1 + length(dataList)), "npc"), vgap =

-  unit(0.3, "lines"), ylabs = "auto", ylabsRot = ifelse(horiz, 0, 90),

-  ylabsPos = unit(2.5, "lines"), xaxis = FALSE, yaxis = FALSE, xlab = "",

-  types = "barplot", heights = NULL, dataColumn = "score", gps = gpar(col =

-  "black", fill = "gray")), colorSheme = gieStain(), gp = gpar(fill =

-  NA, lwd = 2), ...)

+ideogramPlot(

+  ideo,

+  dataList,

+  layout = NULL,

+  horiz = TRUE,

+  parameterList = list(vp = plotViewport(margins = c(0.1, 4.1, 0.3, 0.1)), ideoHeight =

+    unit(1/(1 + length(dataList)), "npc"), vgap = unit(0.3, "lines"), ylabs = "auto",

+    ylabsRot = ifelse(horiz, 0, 90), ylabsPos = unit(2.5, "lines"), xaxis = FALSE, yaxis =

+    FALSE, xlab = "", types = "barplot", heights = NULL, dataColumn = "score", gps =

+    gpar(col = "black", fill = "gray")),

+  colorSheme = gieStain(),

+  gp = gpar(fill = NA, lwd = 2),

+  ...

+)

 }

 \arguments{

 \item{ideo}{output of \link{loadIdeogram}.}

@@ -4,8 +4,13 @@

 \alias{importScore}

 \title{Reading data from a BED or WIG file}

 \usage{

-importScore(file, file2, format = c("BED", "bedGraph", "WIG", "BigWig"),

-  ranges = GRanges(), ignore.strand = TRUE)

+importScore(

+  file,

+  file2,

+  format = c("BED", "bedGraph", "WIG", "BigWig"),

+  ranges = GRanges(),

+  ignore.strand = TRUE

+)

 }

 \arguments{

 \item{file}{The path to the file to read.}

@@ -4,12 +4,25 @@

 \alias{lolliplot}

 \title{Lolliplots}

 \usage{

-lolliplot(SNP.gr, features = NULL, ranges = NULL, type = "circle",

-  newpage = TRUE, ylab = TRUE, ylab.gp = gpar(col = "black"),

-  yaxis = TRUE, yaxis.gp = gpar(col = "black"), xaxis = TRUE,

-  xaxis.gp = gpar(col = "black"), legend = NULL, cex = 1,

-  dashline.col = "gray80", jitter = c("node", "label"),

-  rescale = FALSE, ...)

+lolliplot(

+  SNP.gr,

+  features = NULL,

+  ranges = NULL,

+  type = "circle",

+  newpage = TRUE,

+  ylab = TRUE,

+  ylab.gp = gpar(col = "black"),

+  yaxis = TRUE,

+  yaxis.gp = gpar(col = "black"),

+  xaxis = TRUE,

+  xaxis.gp = gpar(col = "black"),

+  legend = NULL,

+  cex = 1,

+  dashline.col = "gray80",

+  jitter = c("node", "label"),

+  rescale = FALSE,

+  ...

+)

 }

 \arguments{

 \item{SNP.gr}{A object of \link[GenomicRanges:GRanges-class]{GRanges}, 

@@ -4,8 +4,7 @@

 \alias{optimizeStyle}

 \title{Optimize the style of plot}

 \usage{

-optimizeStyle(trackList, viewerStyle = trackViewerStyle(),

-  theme = NULL)

+optimizeStyle(trackList, viewerStyle = trackViewerStyle(), theme = NULL)

 }

 \arguments{

 \item{trackList}{An object of \code{\link{trackList}}}

@@ -4,8 +4,13 @@

 \alias{plotGRanges}

 \title{plot GRanges data}

 \usage{

-plotGRanges(..., range = GRanges(), viewerStyle = trackViewerStyle(),

-  autoOptimizeStyle = FALSE, newpage = TRUE)

+plotGRanges(

+  ...,

+  range = GRanges(),

+  viewerStyle = trackViewerStyle(),

+  autoOptimizeStyle = FALSE,

+  newpage = TRUE

+)

 }

 \arguments{

 \item{\dots}{one or more objects of \code{\link[GenomicRanges:GRanges-class]{GRanges}}}

@@ -4,8 +4,13 @@

 \alias{plotIdeo}

 \title{plot ideogram}

 \usage{

-plotIdeo(ideo, chrom = seqlevels(ideo)[1], colorSheme = gieStain(),

-  gp = gpar(fill = NA), ...)

+plotIdeo(

+  ideo,

+  chrom = seqlevels(ideo)[1],

+  colorSheme = gieStain(),

+  gp = gpar(fill = NA),

+  ...

+)

 }

 \arguments{

 \item{ideo}{output of \link{loadIdeogram}.}

@@ -4,14 +4,19 @@

 \alias{plotOneIdeo}

 \title{plot ideogram with data for one chromosome}

 \usage{

-plotOneIdeo(ideo, dataList, parameterList = list(vp =

-  plotViewport(margins = c(0.1, 4.1, 1.1, 0.1)), ideoHeight = unit(1/(1 +

-  length(dataList)), "npc"), vgap = unit(1, "lines"), ylabs =

-  seqlevels(ideo)[1], ylabsRot = 90, ylabsPos = unit(2.5, "lines"), xaxis =

-  FALSE, yaxis = FALSE, xlab = "", types = "barplot", heights = NULL,

-  dataColumn = "score", gps = gpar(col = "black", fill = "gray")),

-  chrom = seqlevels(ideo)[1], colorSheme = gieStain(), gp = gpar(fill

-  = NA, lwd = 2), ...)

+plotOneIdeo(

+  ideo,

+  dataList,

+  parameterList = list(vp = plotViewport(margins = c(0.1, 4.1, 1.1, 0.1)), ideoHeight =

+    unit(1/(1 + length(dataList)), "npc"), vgap = unit(1, "lines"), ylabs =

+    seqlevels(ideo)[1], ylabsRot = 90, ylabsPos = unit(2.5, "lines"), xaxis = FALSE, yaxis

+    = FALSE, xlab = "", types = "barplot", heights = NULL, dataColumn = "score", gps =

+    gpar(col = "black", fill = "gray")),

+  chrom = seqlevels(ideo)[1],

+  colorSheme = gieStain(),

+  gp = gpar(fill = NA, lwd = 2),

+  ...

+)

 }

 \arguments{

 \item{ideo}{output of \link{loadIdeogram}.}

@@ -101,7 +101,7 @@ the scores of a given track. It should contain score metadata. When dat2

 and dat is paired, dat will be drawn as positive value where dat2 will be 

 drawn as negative value (-1 * score)}

-\item{\code{type}}{The type of track. It could be 'data', 'gene', 'transcript' or 'lollipopData'.}

+\item{\code{type}}{The type of track. It could be 'data', 'gene', 'transcript', 'lollipopData' or 'interactionData'.}

 \item{\code{format}}{The format of the input. It could be "BED", "bedGraph",

 "WIG", "BigWig" or "BAM"}

@@ -13,8 +13,7 @@ trackViewerStyle(...)

 setTrackViewerStyleParam(tvs, attr, value)

-\S4method{setTrackViewerStyleParam}{trackViewerStyle,character}(tvs, attr,

-  value)

+\S4method{setTrackViewerStyleParam}{trackViewerStyle,character}(tvs, attr, value)

 }

 \arguments{

 \item{\dots}{Each argument in \dots becomes an slot in the new trackViewerStyle.}

@@ -4,8 +4,17 @@

 \alias{viewGene}

 \title{plot tracks based on gene name}

 \usage{

-viewGene(symbol, filenames, format, txdb, org, upstream = 1000,

-  downstream = 1000, anchor = c("gene", "TSS"), plot = FALSE)

+viewGene(

+  symbol,

+  filenames,

+  format,

+  txdb,

+  org,

+  upstream = 1000,

+  downstream = 1000,

+  anchor = c("gene", "TSS"),

+  plot = FALSE

+)

 }

 \arguments{

 \item{symbol}{Gene symbol}

@@ -4,10 +4,20 @@

 \alias{viewTracks}

 \title{plot the tracks}

 \usage{

-viewTracks(trackList, chromosome, start, end, strand, gr = GRanges(),

-  ignore.strand = TRUE, viewerStyle = trackViewerStyle(),

-  autoOptimizeStyle = FALSE, newpage = TRUE, operator = NULL,

-  smooth = FALSE)

+viewTracks(

+  trackList,

+  chromosome,

+  start,

+  end,

+  strand,

+  gr = GRanges(),

+  ignore.strand = TRUE,

+  viewerStyle = trackViewerStyle(),

+  autoOptimizeStyle = FALSE,

+  newpage = TRUE,

+  operator = NULL,

+  smooth = FALSE

+)

 }

 \arguments{

 \item{trackList}{an object of \code{\link{trackList}}}

@@ -962,6 +962,18 @@ ideogramPlot(ideo, dataList,

 # Plot genomic interactions data

+Plot genomic interactions data as tracks.

+

+```{r}

+library(InteractionSet)

+gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds", package="trackViewer"))

+range <- GRanges("chr6", IRanges(51120000, 53200000))

+tr <- gi2track(gi)

+ctcf <- readRDS(system.file("extdata", "ctcf.sample.rds", package="trackViewer"))

+viewTracks(trackList(ctcf, tr), gr=range, autoOptimizeStyle = TRUE)

+```

+

+

 Different from most of the available tools, plotGInteractions try to plot the data with the 2D structure. The nodes indicate the region with interactions and

 the edges indicates the interactions. The size of the nodes are relative to the width of the region.

 The features could be the enhancers, promoters or genes. The enhancer and promoter are shown as