fix clusterPlotR

genesofeve · Nov 10, 2017 · 0791303 · 0791303
1 parent aa7ab2e
commit 0791303
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Showing 24 changed files with 64 additions and 19 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: projectR
 Type: Package
 Title: Functions for the projection of weights from PCA, CoGAPS, NMF,
     correlation, and clustering
-Version: 0.99.10
+Version: 0.99.12
 Date: 2016-11-22
 Author: Genevieve Stein-O'Brien
 Maintainer: Genevieve Stein-O'Brien <gsteinobrien@gmail.com>

diff --git a/DESCRIPTION~ b/DESCRIPTION~
@@ -2,26 +2,20 @@ Package: projectR
 Type: Package
 Title: Functions for the projection of weights from PCA, CoGAPS, NMF,
     correlation, and clustering
-Version: 0.99.10
+Version: 0.99.11
 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:
-    RColorBrewer (>= 1.0.5),
     gplots (>= 2.8.0),
     graphics,
     grDevices,
     methods,
     cluster,
-    shiny,
     stats,
     utils,
-    doParallel,
-    foreach,
-    iterators,
-    parallel,
     ggplot2,
     reshape2,
     limma,

diff --git a/NAMESPACE b/NAMESPACE
@@ -23,13 +23,3 @@ export(rotatoR)
 import(limma)
 import(stats)
 importFrom(limma,lmFit)
-import(RColorBrewer)
-import(gplots)
-import(graphics)
-import(grDevices)
-import(methods)
-import(cluster)
-import(utils)    
-import(ggplot2)
-import(reshape2)
-import(MASS)
diff --git a/R/clusterPlotR.R b/R/clusterPlotR.R
@@ -9,7 +9,6 @@
 #' @param ... additional parameters for plotting. ex. pch,cex,col,labels, xlab, etc.
 #' @return A plot of the mean behavior for each cluster 
 #' @export
-#' @examples 
 #' @examples
 #'  k.RNAseq6l3c3t<-kmeans(p.RNAseq6l3c3t,22)
 #'  clusterPlotR(p.RNAseq6l3c3t, cls=k.RNAseq6l3c3t, NC=1,x=pd.RNAseq6l3c3t$days, col=pd.RNAseq6l3c3t$color)
@@ -97,6 +96,8 @@ for(i in cls1){
 #'  clusterPlotR(cData=p, cls=pk, x=jitter(pd$days), col=pd$colors)
 #'}
 
+
+
 clusterPlotR.hclust <- function(
 	cData=NA, # data used to get clusters
 	cls=NA, # an hclust object

diff --git a/man/cluster2pattern.Rd b/man/cluster2pattern.Rd
diff --git a/man/cluster2pattern.hclust.Rd b/man/cluster2pattern.hclust.Rd
diff --git a/man/cluster2pattern.kmeans.Rd b/man/cluster2pattern.kmeans.Rd
diff --git a/man/clusterPlotR.Rd b/man/clusterPlotR.Rd
diff --git a/man/clusterPlotR.hclust.Rd b/man/clusterPlotR.hclust.Rd
diff --git a/man/clusterPlotR.kmeans.Rd b/man/clusterPlotR.kmeans.Rd
diff --git a/man/correlateR.Rd b/man/correlateR.Rd
diff --git a/man/geneMatchR.Rd b/man/geneMatchR.Rd
diff --git a/man/intersectoR.Rd b/man/intersectoR.Rd
diff --git a/man/intersectoR.default.Rd b/man/intersectoR.default.Rd
diff --git a/man/intersectoR.hclust.Rd b/man/intersectoR.hclust.Rd
diff --git a/man/intersectoR.kmeans.Rd b/man/intersectoR.kmeans.Rd
diff --git a/man/projectR.CoGAPS.Rd b/man/projectR.CoGAPS.Rd
diff --git a/man/projectR.Rd b/man/projectR.Rd
diff --git a/man/projectR.correlateR.Rd b/man/projectR.correlateR.Rd
diff --git a/man/projectR.default.Rd b/man/projectR.default.Rd
diff --git a/man/projectR.pclust.Rd b/man/projectR.pclust.Rd
diff --git a/man/projectR.prcomp.Rd b/man/projectR.prcomp.Rd
diff --git a/man/projectR.rotatoR.Rd b/man/projectR.rotatoR.Rd
diff --git a/man/rotatoR.Rd b/man/rotatoR.Rd