Merge pull request #94 from charles-plessy/reverseCumulativesGGplot

Port plotReverseCumulatives to ggplot2

Author: charles-plessy

DESCRIPTION

@@ -26,10 +26,12 @@ Imports:
     KernSmooth,
     memoise,
     plyr,
+    rlang,
     Rsamtools,
     reshape2,
     rtracklayer,
     S4Vectors (>= 0.27.5),
+    scales,
     som,
     stringdist,
     stringi,
@@ -77,7 +79,6 @@ Collate:
     'CumulativeDistributionFunctions.R'
     'GetMethods.R'
     'CumulativeDistributionMethods.R'
-    'ExportFunctions.R'
     'ExportMethods.R'
     'ExpressionProfilingMethods.R'
     'ImportFunctions.R'

NAMESPACE

@@ -146,18 +146,27 @@ importFrom(data.table,setkeyv)
 importFrom(data.table,setnames)
 importFrom(formula.tools,lhs)
 importFrom(formula.tools,rhs.vars)
+importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_abline)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_histogram)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_segment)
+importFrom(ggplot2,geom_step)
+importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,guide_legend)
+importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,position_stack)
+importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_x_log10)
+importFrom(ggplot2,scale_y_log10)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
 importFrom(grDevices,blues9)
@@ -170,23 +179,23 @@ importFrom(grDevices,rainbow)
 importFrom(grDevices,rgb)
 importFrom(grDevices,xy.coords)
 importFrom(graphics,Axis)
-importFrom(graphics,abline)
 importFrom(graphics,axis)
 importFrom(graphics,box)
 importFrom(graphics,legend)
 importFrom(graphics,lines)
 importFrom(graphics,mtext)
 importFrom(graphics,pairs)
 importFrom(graphics,par)
-importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(graphics,strwidth)
 importFrom(graphics,text)
 importFrom(gtools,mixedorder)
 importFrom(memoise,memoise)
 importFrom(plyr,ddply)
 importFrom(reshape2,melt)
+importFrom(rlang,.data)
 importFrom(rtracklayer,import.bed)
+importFrom(scales,hue_pal)
 importFrom(som,som)
 importFrom(stats,coefficients)
 importFrom(stats,cor)

R/CorrelationMethods.R

@@ -71,6 +71,7 @@
 #' 
 #' plotCorrelation2(exampleCAGEexp, what = "consensusClusters", value = "normalized")
 #' 
+#' @importFrom graphics box legend par strwidth text
 #' @export
 
 setGeneric( "plotCorrelation"