Added NEWS file. More specific imports and exports. Added example to addlegend.

Author: dphansti

DESCRIPTION

@@ -2,7 +2,7 @@ Package: Sushi
 Type: Package
 Title: Tools for visualizing genomics data
 Description: Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures
-Version: 0.99.0
+Version: 0.99.1
 Date: 2014-02-17
 Author: Douglas H Phanstiel <[email protected]>
 Maintainer: Douglas H Phanstiel <[email protected]>

NAMESPACE

@@ -1,4 +1,13 @@
-exportPattern("^[[:alpha:]]+")
 
-import(biomaRt)
-import(zoo)
+importFrom(biomaRt, getBM, useMart)
+importFrom(graphics, abline, arrows, axis, curve, hist, mtext, par,
+           plot, points, polygon, rect, segments, text)
+importFrom(grDevices, col2rgb, colorRampPalette, rgb, topo.colors)
+importFrom(zoo, rollapply)
+
+export(addlegend  ,labelgenome ,labelplot ,maptocolors ,
+maptolwd ,opaque ,plotBed ,plotBedgraph ,plotBedpe ,
+plotGenes ,plotHic ,plotManhattan ,SushiColors ,
+zoombox ,zoomsregion)
+
+

NEWS.md

@@ -0,0 +1,20 @@
+Sushi News
+==========
+
+CHANGES IN R 0.99.1:
+
+    * Made package lighter by adding more specific imports and exports
+    
+    * added examples for all exported functions
+
+Sushi
+=====
+
+Package: Sushi
+Title: Tools for visualizing genomics data
+Description: Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures
+Author: Douglas H Phanstiel <[email protected]>
+Maintainer: Douglas H Phanstiel <[email protected]>
+biocViews: DataRepresentation, Visualization, Genetics, Sequencing, Infrastructure,
+License: GPL (>= 2)
+Depends: R (>= 2.10), zoo,biomaRt

R/addlegend.R

@@ -20,7 +20,20 @@
 #' @param title.font font type of legend title
 #' @param title.cex font size of legned text
 #' @export
-
+#' @examples
+#' 
+#' data(Sushi_HiC.matrix)
+#' 
+#' chrom            = "chr11"
+#' chromstart       = 500000
+#' chromend         = 5050000
+#' 
+#' phic = plotHic(Sushi_HiC.matrix,chrom,chromstart,chromend,max_y = 20,zrange=c(0,28),palette = topo.colors,flip=FALSE)
+#' 
+#' labelgenome(chrom,chromstart,chromend,side=1,scipen=20,n=4,scale="Mb",edgeblankfraction=0.20,line=.18,chromline=.5,scaleline=0.5)
+#' 
+#' addlegend(phic[[1]],palette=phic[[2]],title="score",side="right",bottominset=0.4,topinset=0,xoffset=-.035,labelside="left",width=0.025,title.offset=0.035)
+#'
 addlegend <-
   function(range,title="",labels.digits=1,palette=topo.colors,side="right",labelside="left",
            xoffset=0.1,width=0.05,bottominset=0.025,topinset=0.025,tick.num = 5,tick.length=0.01,

README.md

@@ -52,4 +52,17 @@ addlegend(range, title = "", labels.digits = 1, palette = topo.colors,
 This function adds a legend to Sushi plots that have a
 colorby function (e.g. plotHic, plotGenes, and plotBedpe)
 }
+\examples{
+data(Sushi_HiC.matrix)
+
+chrom            = "chr11"
+chromstart       = 500000
+chromend         = 5050000
+
+phic = plotHic(Sushi_HiC.matrix,chrom,chromstart,chromend,max_y = 20,zrange=c(0,28),palette = topo.colors,flip=FALSE)
+
+labelgenome(chrom,chromstart,chromend,side=1,scipen=20,n=4,scale="Mb",edgeblankfraction=0.20,line=.18,chromline=.5,scaleline=0.5)
+
+addlegend(phic[[1]],palette=phic[[2]],title="score",side="right",bottominset=0.4,topinset=0,xoffset=-.035,labelside="left",width=0.025,title.offset=0.035)
+}