update version

Former-commit-id: 5143e44

DESCRIPTION

@@ -2,24 +2,23 @@ Package: projectR
 Type: Package
 Title: Functions for the projection of weights from PCA, CoGAPS, NMF,
     correlation, and clustering
-Version: 0.99.14
+Version: 0.99.15
 Date: 2016-11-22
 Author: Genevieve Stein-O'Brien
 Maintainer: Genevieve Stein-O'Brien <gsteinobrien@gmail.com>
 Description: Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.
 License: GPL (==2)
 Imports:
-    gplots (>= 2.8.0),
     graphics,
     grDevices,
     methods,
     cluster,
     stats,
     utils,
-    ggplot2,
-    reshape2,
     limma,
-    MASS
+    MASS,
+    ggplot2,
+    reshape2
 Suggests:
     CoGAPS,
     BiocStyle,

DESCRIPTION~

@@ -2,24 +2,23 @@ Package: projectR
 Type: Package
 Title: Functions for the projection of weights from PCA, CoGAPS, NMF,
     correlation, and clustering
-Version: 0.99.13
+Version: 0.99.14
 Date: 2016-11-22
 Author: Genevieve Stein-O'Brien
 Maintainer: Genevieve Stein-O'Brien <gsteinobrien@gmail.com>
 Description: Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.
 License: GPL (==2)
 Imports:
-    gplots (>= 2.8.0),
     graphics,
     grDevices,
     methods,
     cluster,
     stats,
     utils,
-    ggplot2,
-    reshape2,
     limma,
-    MASS
+    MASS,
+    ggplot2,
+    reshape2
 Suggests:
     CoGAPS,
     BiocStyle,

NAMESPACE

@@ -20,7 +20,14 @@ export(geneMatchR)
 export(intersectoR)
 export(projectR)
 export(rotatoR)
+import(MASS)
+import(cluster)
+import(ggplot2)
+import(grDevices)
 import(graphics)
 import(limma)
+import(methods)
+import(reshape2)
 import(stats)
+import(utils)
 importFrom(limma,lmFit)

R/clusterPlotR.R

@@ -10,6 +10,8 @@
 #' @return A plot of the mean behavior for each cluster
 #' @export
 #' @import graphics
+#' @import ggplot2
+#' @import reshape2
 #' @examples \dontrun{
 #'  k.RNAseq6l3c3t<-kmeans(p.RNAseq6l3c3t,22)
 #'  clusterPlotR(p.RNAseq6l3c3t, cls=k.RNAseq6l3c3t, NC=2,x=pd.RNAseq6l3c3t$days, col=pd.RNAseq6l3c3t$color)

R/projectR.R

@@ -15,6 +15,9 @@
 #' @import limma
 #' @importFrom limma lmFit
 #' @import stats
+#' @import grDevices
+#' @import methods
+#' @import utils
 #' @export
 
 
@@ -143,6 +146,7 @@ projectR.CoGAPS <- function(
 #'                              AnnotionObj=map.ESepiGen4c1l,IDcol="GeneSymbols")
 #'
 #' @import limma
+#' @import cluster
 #' @import stats
 #' @export
 
@@ -191,9 +195,10 @@ projectR.pclust <- function(
 #'  pca.RNAseq6l3c3t<-prcomp(t(p.RNAseq6l3c3t))
 #'  pca.ESepiGen4c1l<-projectR(data=p.ESepiGen4c1l$mRNA.Seq,Patterns=pca.RNAseq6l3c3t,
 #'                                AnnotionObj=map.ESepiGen4c1l,IDcol="GeneSymbols")
-#' 
+#'
 #' @import limma
 #' @import stats
+#' @import MASS
 #' @export
 
 
@@ -248,7 +253,7 @@ projectR.prcomp <- function(
 #'  r.RNAseq6l3c3t<-rotatoR(1,1,-1,-1,pca.RNAseq6l3c3t$x[,1:2])
 #'  pca.ESepiGen4c1l<-projectR(data=p.ESepiGen4c1l$mRNA.Seq,Patterns=r.RNAseq6l3c3t,
 #'                          AnnotionObj=map.ESepiGen4c1l,IDcol="GeneSymbols")
-#' 
+#'
 #' @import stats
 #' @export
 
@@ -304,7 +309,7 @@ projectR.rotatoR <- function(
 #'  c.RNAseq6l3c3t<-correlateR(genes="T", dat=p.RNAseq6l3c3t, threshtype="N", threshold=10, absR=TRUE)
 #'  cor.ESepiGen4c1l<-projectR(data=p.ESepiGen4c1l$mRNA.Seq,Patterns=c.RNAseq6l3c3t,NP="PositiveCOR",
 #'                                    AnnotionObj=map.ESepiGen4c1l,IDcol="GeneSymbols")
-#' 
+#'
 #' @import limma
 #' @import stats
 #' @export