updated namespace

ajitjohnson · Jun 17, 2020 · aed10fd · aed10fd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7  1,7 @@
 Package: arseq
 Type: Package
 Title: Automated RNA Sequencing Analysis Pipeline
-Version: 2.2.1
 Version: 2.2.2
 Author: Ajit Johnson Nirmal
 Maintainer: Ajit Johnson Nirmal <[email protected]>
 Description: Biologist friendly program that supports the following analysis in an automated fashion with minimal coding requirement. 
@@ -24,6  24,7 @@ Description: Biologist friendly program that supports the following analysis in
     Kyoto Encyclopedia of Genes and Genomes pathway enrichment of the differentially expressed genes.
     Kyoto Encyclopedia of Genes and Genomes pathway diagrams of the top 5 enriched pathways. 
     Gene Set Enrichment Analysis (H, C1, C2, C3, C4, C5, C6, C7 gene set).
     Reactome Enrichment Analysis
     Custom Gene Set Enrichment Analysis.
 License: GPL-3
 Encoding: UTF-8
@@ -62,6  63,6 @@ Imports:
   ComplexHeatmap (>= 2.5.2),
   clusterProfiler (>= 3.14.3),
   ReactomePA (>= 1.30.0)
-RoxygenNote: 6.1.1
 RoxygenNote: 7.0.2
 URL: https://github.com/ajitjohnson/arseq
 Suggests: testthat
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4  1,4 @@
-# Generated by roxygen2: do not edit by hand
 # Generated by roxygen2: do not edit by hand
 
 export(arseq)
 export(arseq.ensembl2genename)
@@ -11,18  11,26 @@ export(arseq.gsea.preprocess)
 export(arseq.gsea.runall)
 export(arseq.kegg.enrich)
 export(arseq.kegg.enrich.plot)
 export(arseq.kmeans)
 export(arseq.kmeans.plot)
 export(arseq.kmeans.reactome.plot)
 export(arseq.mds.plot)
 export(arseq.mvg)
 export(arseq.mvg.plot)
 export(arseq.pca)
 export(arseq.pca.plot)
 export(arseq.poisd.dist)
 export(arseq.poisd.dist.plot)
 export(arseq.reactome.enrich)
 export(arseq.volcano.plot)
 import(ComplexHeatmap)
 import(DESeq2)
 import(EnhancedVolcano)
 import(PoiClaClu)
 import(RColorBrewer)
 import(ReactomePA)
 import(circlize)
 import(clusterProfiler)
 import(fgsea)
 import(gage)
 import(ggplot2)
@@ -54,6  62,7 @@ importFrom(stats,cmdscale)
 importFrom(stats,complete.cases)
 importFrom(stats,dist)
 importFrom(stats,hclust)
 importFrom(stats,kmeans)
 importFrom(stats,na.omit)
 importFrom(stats,prcomp)
 importFrom(stats,var)
diff --git a/R/arseq.kmeans.plot.R b/R/arseq.kmeans.plot.R
@@ -2,10  2,10 @@
 #' @description Heatmap of the Most Variable genes divided into clusters
 #' @param data Normalized expression dataframe
 #' @param clusters List of gene clusters returned by Kmeans clustering algorithm
-#' @return Kmeans clusters
 #' @import ComplexHeatmap
 #' @import circlize
 #' @import RColorBrewer
 #' @return Heatmap
 #' @examples
 #' arseq.kmeans.plot (data,clusters=kmeansclusters,metadata= example_meta,intgroup="treatment")
 #' @export
@@ -18,7  18,6 @@ arseq.kmeans.plot <- function(data, clusters, metadata,
   clusters <- data.frame(clusters)
 
   # Set the colors for heatmap
-  require(circlize)
   h1_col = colorRamp2(c(-2, -1, 0, 1, 2), c("#4B6AAF",  '#55B0AE', "#F8F6B8","#F5A15B","#B11E4B"))
 
   # Add Row annotation (clusters)

diff --git a/man/arseq.Rd b/man/arseq.Rd
diff --git a/man/arseq.deg.plot.Rd b/man/arseq.deg.plot.Rd
diff --git a/man/arseq.ensembl2genename.Rd b/man/arseq.ensembl2genename.Rd
diff --git a/man/arseq.euclid.dist.Rd b/man/arseq.euclid.dist.Rd
diff --git a/man/arseq.euclid.dist.plot.Rd b/man/arseq.euclid.dist.plot.Rd