diff --git a/DESCRIPTION b/DESCRIPTION
index 4923271..1e28fb6 100644
--- 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 <ajitjohnson.n@gmail.com>
 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
index 00f290b..3d788fa 100644
--- 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)
@@ -11,6 +11,9 @@ 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)
@@ -18,11 +21,16 @@ 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
index e74f403..d0a9426 100644
--- 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
index 24a2e33..f26630f 100644
--- a/man/arseq.Rd
+++ b/man/arseq.Rd
@@ -1,43 +1,59 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.R
-\name{arseq}
-\alias{arseq}
-\title{Automated RNASeq Analysis Pipeline}
-\usage{
-arseq(data, meta, design, contrast, qc = TRUE, dgea = TRUE,
-  variable.genes = 1000, folder.name = "ARSeq", custom.gsea = NULL,
-  save.dir = getwd())
-}
-\arguments{
-\item{data}{Un-normalized counts matrix (please note that you should NOT pass in normalized data).  The counts' table should contain unique gene names as the first column. ENSEMBL ID's are also allowed but no other form of ID's are currently supported. Check example- head(example_data): \code{\link{example_data}}.}
-
-\item{meta}{A CSV file with information regarding the samples. It is absolutely critical that the columns of the counts' matrix and the rows of the metadata are in the same order. The function will not make guesses as to which column of the count matrix belongs to which row of the metadata, these must be provided in a consistent order. Check example- head(example_meta): \code{\link{example_meta}}.}
-
-\item{design}{The formula that expresses how the counts for each gene depend on your metadata (used to calculate the necessary data for differential gene expression analysis). Check DESeq2 documentation for designing the formula. In general, you pass in a column name (e.g. treatment) of your metadata file or a combination of column names (e.g. treatment + cell_type).}
-
-\item{contrast}{Information regarding the groups between which you would like to perform differential gene expression analysis. It could be between two groups or between multiple groups and needs to follow the following format: contrast = list(A = c(" "), B= c(" ")). If you are comparing two groups (e.g. control vs treatment), the constrast argument should look like the following: contrast = list(A = c("control"), B= c("treatment")). In situations where you have multiple groups to compare- (e.g. control vs treatment1 and treatment2), you should do the following- contrast = list(A = c("control"), B= c("treatment1", "treatment2")).}
-
-\item{qc}{Logical. When passed in TRUE, the program would run the quality control modules on the entire dataset. If you are planning to perform multiple comparisons using the contrast argument, run  qc = TRUE for the first time and then change it to qc = FALSE for the subsequent comparisons to speed up the analysis.}
-
-\item{dgea}{Logical. Parameter to define if differential gene expression analysis is to be performed. Default: TRUE}
-
-\item{variable.genes}{numeric: The number of most variable genes to be identified. By default, the program identifies the top 1000 most variable genes.}
-
-\item{folder.name}{Custom folder name that you would like to save your results in.}
-
-\item{custom.gsea}{User defined gene list to perform GSEA. File need to be supplied as a dataframe with each row as a gene list}
-
-\item{save.dir}{Directory to save the results in. Default: Working Directory.}
-}
-\value{
-Differentially expressed genes.
-}
-\description{
-An easy to use pipeline for analysing RNA Seq data. The package currently supports the following analysis- Differential gene expression analysis using DESeq2, Calculate the most variable genes, PCA analysis, GO enrichment of the differentially expressed genes, KEGG pathway enrichment of the differentially expressed genes, GSEA analysis.
-}
-\examples{
-\dontrun{
-contrast = list(A = c("control"), B= c("drug_A"))
-arseq2 (data = example_data,meta = example_meta, design = "treatment", contrast = contrast)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.R
+\name{arseq}
+\alias{arseq}
+\title{Automated RNASeq Analysis Pipeline}
+\usage{
+arseq(
+  data,
+  meta,
+  design,
+  contrast,
+  dds = NULL,
+  qc = TRUE,
+  dgea = TRUE,
+  variable.genes = 1000,
+  folder.name = "ARSeq",
+  custom.gsea = NULL,
+  kmeans = 10,
+  save.dir = getwd(),
+  ensemblmirror = "useast"
+)
+}
+\arguments{
+\item{data}{Un-normalized counts matrix (please note that you should NOT pass in normalized data).  The counts' table should contain unique gene names as the first column. ENSEMBL ID's are also allowed but no other form of ID's are currently supported. Check example- head(example_data): \code{\link{example_data}}.}
+
+\item{meta}{A CSV file with information regarding the samples. It is absolutely critical that the columns of the counts' matrix and the rows of the metadata are in the same order. The function will not make guesses as to which column of the count matrix belongs to which row of the metadata, these must be provided in a consistent order. Check example- head(example_meta): \code{\link{example_meta}}.}
+
+\item{design}{The formula that expresses how the counts for each gene depend on your metadata (used to calculate the necessary data for differential gene expression analysis). Check DESeq2 documentation for designing the formula. In general, you pass in a column name (e.g. treatment) of your metadata file or a combination of column names (e.g. treatment + cell_type).}
+
+\item{contrast}{Information regarding the groups between which you would like to perform differential gene expression analysis. It could be between two groups or between multiple groups and needs to follow the following format: contrast = list(A = c(" "), B= c(" ")). If you are comparing two groups (e.g. control vs treatment), the constrast argument should look like the following: contrast = list(A = c("control"), B= c("treatment")). In situations where you have multiple groups to compare- (e.g. control vs treatment1 and treatment2), you should do the following- contrast = list(A = c("control"), B= c("treatment1", "treatment2")).}
+
+\item{qc}{Logical. When passed in TRUE, the program would run the quality control modules on the entire dataset. If you are planning to perform multiple comparisons using the contrast argument, run  qc = TRUE for the first time and then change it to qc = FALSE for the subsequent comparisons to speed up the analysis.}
+
+\item{dgea}{Logical. Parameter to define if differential gene expression analysis is to be performed. Default: TRUE}
+
+\item{variable.genes}{numeric: The number of most variable genes to be identified. By default, the program identifies the top 1000 most variable genes.}
+
+\item{folder.name}{Custom folder name that you would like to save your results in.}
+
+\item{custom.gsea}{User defined gene list to perform GSEA. File need to be supplied as a dataframe with each row as a gene list}
+
+\item{kmeans}{int. Number of clusters/ gene modules. The Most Variable Genes and Differentially Expressed Genes will be divided into the user defined clusters. Default 10.}
+
+\item{save.dir}{Directory to save the results in. Default: Working Directory.}
+
+\item{ensemblmirror}{String. Values for the mirror argument are: useast, uswest, asia}
+}
+\value{
+Differentially expressed genes.
+}
+\description{
+An easy to use pipeline for analysing RNA Seq data. The package currently supports the following analysis- Differential gene expression analysis using DESeq2, Calculate the most variable genes, PCA analysis, GO enrichment of the differentially expressed genes, KEGG pathway enrichment of the differentially expressed genes, GSEA analysis.
+}
+\examples{
+\dontrun{
+contrast = list(A = c("control"), B= c("drug_A"))
+arseq2 (data = example_data,meta = example_meta, design = "treatment", contrast = contrast)
+}
 }
diff --git a/man/arseq.deg.plot.Rd b/man/arseq.deg.plot.Rd
index 1ad0e09..d011d21 100644
--- a/man/arseq.deg.plot.Rd
+++ b/man/arseq.deg.plot.Rd
@@ -1,25 +1,25 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.deg.plot.R
-\name{arseq.deg.plot}
-\alias{arseq.deg.plot}
-\title{Heatmap of the differentially expressed genes}
-\usage{
-arseq.deg.plot(deg, data, dds, save.plot = FALSE, save.dir = getwd())
-}
-\arguments{
-\item{deg}{Differtially expressed genes calculated using DESeq2}
-
-\item{data}{Normalized count's matrix}
-
-\item{dds}{DeSes2 object}
-
-\item{save.plot}{Logical. Argument to state if the plot needs to be saved in disk. Default: FALSE}
-
-\item{save.dir}{Location to save the plot when 'save.plot=TRUE'. Default: Working Directory.}
-}
-\value{
-Heatmap of the differentially expressed genes.
-}
-\description{
-Generating a heatmap of the differentially expressed genes
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.deg.plot.R
+\name{arseq.deg.plot}
+\alias{arseq.deg.plot}
+\title{Heatmap of the differentially expressed genes}
+\usage{
+arseq.deg.plot(deg, data, dds, save.plot = FALSE, save.dir = getwd())
+}
+\arguments{
+\item{deg}{Differtially expressed genes calculated using DESeq2}
+
+\item{data}{Normalized count's matrix}
+
+\item{dds}{DeSes2 object}
+
+\item{save.plot}{Logical. Argument to state if the plot needs to be saved in disk. Default: FALSE}
+
+\item{save.dir}{Location to save the plot when 'save.plot=TRUE'. Default: Working Directory.}
+}
+\value{
+Heatmap of the differentially expressed genes.
+}
+\description{
+Generating a heatmap of the differentially expressed genes
 }
diff --git a/man/arseq.ensembl2genename.Rd b/man/arseq.ensembl2genename.Rd
index 7f5e8cf..524b11b 100644
--- a/man/arseq.ensembl2genename.Rd
+++ b/man/arseq.ensembl2genename.Rd
@@ -1,22 +1,22 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.ensembl2genename.R
-\name{arseq.ensembl2genename}
-\alias{arseq.ensembl2genename}
-\title{Gene ID converter}
-\usage{
-arseq.ensembl2genename(data)
-}
-\arguments{
-\item{data}{Expression matrix with ensemble id's as the first column}
-}
-\value{
-Expression matrix with gene names as the first column
-}
-\description{
-Convert ensembl id's to hugo gene names. The function also reduces multiple transcripts into a single gene by taking the sum of all transcripts.
-}
-\examples{
-\dontrun{
-data <- arseq.ensembl2genename (example_data)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.ensembl2genename.R
+\name{arseq.ensembl2genename}
+\alias{arseq.ensembl2genename}
+\title{Gene ID converter}
+\usage{
+arseq.ensembl2genename(data, ensemblmirror)
+}
+\arguments{
+\item{data}{Expression matrix with ensemble id's as the first column}
+}
+\value{
+Expression matrix with gene names as the first column
+}
+\description{
+Convert ensembl id's to hugo gene names. The function also reduces multiple transcripts into a single gene by taking the sum of all transcripts.
+}
+\examples{
+\dontrun{
+data <- arseq.ensembl2genename (example_data)
+}
 }
diff --git a/man/arseq.euclid.dist.Rd b/man/arseq.euclid.dist.Rd
index a4e7fe3..421d568 100644
--- a/man/arseq.euclid.dist.Rd
+++ b/man/arseq.euclid.dist.Rd
@@ -1,22 +1,22 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.euclid.dist.R
-\name{arseq.euclid.dist}
-\alias{arseq.euclid.dist}
-\title{Euclidean distance}
-\usage{
-arseq.euclid.dist(dds)
-}
-\arguments{
-\item{dds}{DESeq2 object}
-}
-\value{
-Euclidean distance matrix
-}
-\description{
-Calculate the Euclidean distance between samples.
-}
-\examples{
-\dontrun{
-euclid.dist <- arseq.euclid.dist (example_dds)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.euclid.dist.R
+\name{arseq.euclid.dist}
+\alias{arseq.euclid.dist}
+\title{Euclidean distance}
+\usage{
+arseq.euclid.dist(dds)
+}
+\arguments{
+\item{dds}{DESeq2 object}
+}
+\value{
+Euclidean distance matrix
+}
+\description{
+Calculate the Euclidean distance between samples.
+}
+\examples{
+\dontrun{
+euclid.dist <- arseq.euclid.dist (example_dds)
+}
 }
diff --git a/man/arseq.euclid.dist.plot.Rd b/man/arseq.euclid.dist.plot.Rd
index f0a590f..fa24179 100644
--- a/man/arseq.euclid.dist.plot.Rd
+++ b/man/arseq.euclid.dist.plot.Rd
@@ -1,23 +1,23 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.euclid.dist.plot.R
-\name{arseq.euclid.dist.plot}
-\alias{arseq.euclid.dist.plot}
-\title{Euclidean distance heatmap}
-\usage{
-arseq.euclid.dist.plot(euclid.dist)
-}
-\arguments{
-\item{euclid.dist}{Euclidean distance matrix.}
-}
-\value{
-Euclidean distance heatmap.
-}
-\description{
-Plots a heatmap of the distance between samples using pheatmap.
-}
-\examples{
-\dontrun{
-euclid.dist <- arseq.euclid.dist (example_dds)
-euclid.plot <- arseq.euclid.dist.plot (euclid.dist)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.euclid.dist.plot.R
+\name{arseq.euclid.dist.plot}
+\alias{arseq.euclid.dist.plot}
+\title{Euclidean distance heatmap}
+\usage{
+arseq.euclid.dist.plot(euclid.dist)
+}
+\arguments{
+\item{euclid.dist}{Euclidean distance matrix.}
+}
+\value{
+Euclidean distance heatmap.
+}
+\description{
+Plots a heatmap of the distance between samples using pheatmap.
+}
+\examples{
+\dontrun{
+euclid.dist <- arseq.euclid.dist (example_dds)
+euclid.plot <- arseq.euclid.dist.plot (euclid.dist)
+}
 }
diff --git a/man/arseq.go.enrich.Rd b/man/arseq.go.enrich.Rd
index 44d1084..992e148 100644
--- a/man/arseq.go.enrich.Rd
+++ b/man/arseq.go.enrich.Rd
@@ -1,24 +1,24 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.go.enrich.R
-\name{arseq.go.enrich}
-\alias{arseq.go.enrich}
-\title{Gene Ontology (GO) term enrichment}
-\usage{
-arseq.go.enrich(deg, Padj = 0.05)
-}
-\arguments{
-\item{deg}{Differentially expressed genes dataframe returned by DESeq2 analysis}
-
-\item{Padj}{Numeric. Adjusted P Value cut off to define the differentially expressed genes. Default = 0.05}
-}
-\value{
-Enrichment dataframe
-}
-\description{
-Performing GO term enrichment analysis on the significantly differentially expressed genes.
-}
-\examples{
-\dontrun{
-go.enrich <- arseq.go.enrich (example_deg)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.go.enrich.R
+\name{arseq.go.enrich}
+\alias{arseq.go.enrich}
+\title{Gene Ontology (GO) term enrichment}
+\usage{
+arseq.go.enrich(deg, Padj = 0.05)
+}
+\arguments{
+\item{deg}{Differentially expressed genes dataframe returned by DESeq2 analysis}
+
+\item{Padj}{Numeric. Adjusted P Value cut off to define the differentially expressed genes. Default = 0.05}
+}
+\value{
+Enrichment dataframe
+}
+\description{
+Performing GO term enrichment analysis on the significantly differentially expressed genes.
+}
+\examples{
+\dontrun{
+go.enrich <- arseq.go.enrich (example_deg)
+}
 }
diff --git a/man/arseq.go.enrich.plot.Rd b/man/arseq.go.enrich.plot.Rd
index ca18a68..3e2cc54 100644
--- a/man/arseq.go.enrich.plot.Rd
+++ b/man/arseq.go.enrich.plot.Rd
@@ -1,23 +1,23 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.go.enrich.plot.R
-\name{arseq.go.enrich.plot}
-\alias{arseq.go.enrich.plot}
-\title{Gene Ontology (GO) term enrichment}
-\usage{
-arseq.go.enrich.plot(go.enrich)
-}
-\arguments{
-\item{go.enrich}{Enrichment dataframe. Output of the function 'arseq.go.enrich'}
-}
-\value{
-GO enrichment plot
-}
-\description{
-Plotting the top 5 enriched term from each category
-}
-\examples{
-\dontrun{
-go.enrich <- arseq.go.enrich (example_deg)
-go.plot <- arseq.go.enrich.plot (go.enrich)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.go.enrich.plot.R
+\name{arseq.go.enrich.plot}
+\alias{arseq.go.enrich.plot}
+\title{Gene Ontology (GO) term enrichment}
+\usage{
+arseq.go.enrich.plot(go.enrich)
+}
+\arguments{
+\item{go.enrich}{Enrichment dataframe. Output of the function 'arseq.go.enrich'}
+}
+\value{
+GO enrichment plot
+}
+\description{
+Plotting the top 5 enriched term from each category
+}
+\examples{
+\dontrun{
+go.enrich <- arseq.go.enrich (example_deg)
+go.plot <- arseq.go.enrich.plot (go.enrich)
+}
 }
diff --git a/man/arseq.gsea.Rd b/man/arseq.gsea.Rd
index 5e5f922..d0dc467 100644
--- a/man/arseq.gsea.Rd
+++ b/man/arseq.gsea.Rd
@@ -1,37 +1,44 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.gsea.R
-\name{arseq.gsea}
-\alias{arseq.gsea}
-\title{Gene Set Enrichment Analysis (GSEA)}
-\usage{
-arseq.gsea(ranked.list, custom.gsea = NULL, f.name = "GeneSet",
-  fsub.name = "enrichment", category = NULL, subcategory = NULL,
-  save = FALSE, save.dir = getwd())
-}
-\arguments{
-\item{ranked.list}{Ranked list of genes for GSEA analysis. Use 'arseq.gsea.preprocess' to generate ranked list of genes from DESeq2 differential gene expression analysis.}
-
-\item{custom.gsea}{User defined gene list to perform GSEA. File need to be supplied as a dataframe with each row as a gene list}
-
-\item{f.name}{Folder name to save the results when 'save=TRUE'}
-
-\item{fsub.name}{File name of the results when 'save=TRUE'}
-
-\item{category}{collection, such as H, C1, C2, C3, C4, C5, C6, C7}
-
-\item{subcategory}{sub-collection, such as CGP, MIR, BP, etc}
-
-\item{save}{Logical. Argument to indicate if to save the results in disk (pdf and csv files). Default=FALSE}
-
-\item{save.dir}{Directory to save the results when 'save=TRUE'. Default= Working Directory.}
-}
-\value{
-List containing a dataframe and a ggplot object.
-}
-\description{
-Performing GSEA enrichment analysis on a ranked list of genes.
-}
-\examples{
-ranked.list <- arseq.gsea.preprocess (deg=example_deg)
-gsea.output <- arseq.gsea (ranked.list, category = "H")
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.gsea.R
+\name{arseq.gsea}
+\alias{arseq.gsea}
+\title{Gene Set Enrichment Analysis (GSEA)}
+\usage{
+arseq.gsea(
+  ranked.list,
+  custom.gsea = NULL,
+  f.name = "GeneSet",
+  fsub.name = "enrichment",
+  category = NULL,
+  subcategory = NULL,
+  save = FALSE,
+  save.dir = getwd()
+)
+}
+\arguments{
+\item{ranked.list}{Ranked list of genes for GSEA analysis. Use 'arseq.gsea.preprocess' to generate ranked list of genes from DESeq2 differential gene expression analysis.}
+
+\item{custom.gsea}{User defined gene list to perform GSEA. File need to be supplied as a dataframe with each row as a gene list}
+
+\item{f.name}{Folder name to save the results when 'save=TRUE'}
+
+\item{fsub.name}{File name of the results when 'save=TRUE'}
+
+\item{category}{collection, such as H, C1, C2, C3, C4, C5, C6, C7}
+
+\item{subcategory}{sub-collection, such as CGP, MIR, BP, etc}
+
+\item{save}{Logical. Argument to indicate if to save the results in disk (pdf and csv files). Default=FALSE}
+
+\item{save.dir}{Directory to save the results when 'save=TRUE'. Default= Working Directory.}
+}
+\value{
+List containing a dataframe and a ggplot object.
+}
+\description{
+Performing GSEA enrichment analysis on a ranked list of genes.
+}
+\examples{
+ranked.list <- arseq.gsea.preprocess (deg=example_deg)
+gsea.output <- arseq.gsea (ranked.list, category = "H")
 }
diff --git a/man/arseq.gsea.preprocess.Rd b/man/arseq.gsea.preprocess.Rd
index 091306f..87ab309 100644
--- a/man/arseq.gsea.preprocess.Rd
+++ b/man/arseq.gsea.preprocess.Rd
@@ -1,20 +1,20 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.gsea.preprocess.R
-\name{arseq.gsea.preprocess}
-\alias{arseq.gsea.preprocess}
-\title{GSEA pre-processing step}
-\usage{
-arseq.gsea.preprocess(deg)
-}
-\arguments{
-\item{deg}{Differentially expressed genes dataframe returned by DESeq2 analysis.}
-}
-\value{
-ranked list of genes.
-}
-\description{
-Function takes in the differentially expressed genes from DESEq2 and produces a ranked list for GSEA.
-}
-\examples{
-ranked.list <- arseq.gsea.preprocess (deg=example_deg)
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.gsea.preprocess.R
+\name{arseq.gsea.preprocess}
+\alias{arseq.gsea.preprocess}
+\title{GSEA pre-processing step}
+\usage{
+arseq.gsea.preprocess(deg)
+}
+\arguments{
+\item{deg}{Differentially expressed genes dataframe returned by DESeq2 analysis.}
+}
+\value{
+ranked list of genes.
+}
+\description{
+Function takes in the differentially expressed genes from DESEq2 and produces a ranked list for GSEA.
+}
+\examples{
+ranked.list <- arseq.gsea.preprocess (deg=example_deg)
 }
diff --git a/man/arseq.gsea.runall.Rd b/man/arseq.gsea.runall.Rd
index c7d1ee5..e9321ce 100644
--- a/man/arseq.gsea.runall.Rd
+++ b/man/arseq.gsea.runall.Rd
@@ -1,30 +1,34 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.gsea.runall.R
-\name{arseq.gsea.runall}
-\alias{arseq.gsea.runall}
-\title{Bulk Gene Set Enrichment Analysis (GSEA)}
-\usage{
-arseq.gsea.runall(ranked.list, save = FALSE, custom.gsea = NULL,
-  save.dir = getwd())
-}
-\arguments{
-\item{ranked.list}{Ranked list of genes for GSEA analysis. Use 'arseq.gsea.preprocess' to generate ranked list of genes from DESeq2 differential gene expression analysis.}
-
-\item{save}{Logical. Argument to indicate if to save the results in disk (pdf and csv files). Default=FALSE}
-
-\item{custom.gsea}{User defined gene list to perform GSEA. File need to be supplied as a dataframe with each row as a gene list.}
-
-\item{save.dir}{Directory to save the results when 'save=TRUE'. Default= Working Directory.}
-}
-\value{
-List containing all the GSEA dataframe and ggplot objects.
-}
-\description{
-Performing GSEA enrichment analysis on a ranked list of genes for all msigDB.
-}
-\examples{
-\dontrun{
-ranked.list <- arseq.gsea.preprocess (deg=example_deg)
-gsea.output <- arseq.gsea.runall (ranked.list)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.gsea.runall.R
+\name{arseq.gsea.runall}
+\alias{arseq.gsea.runall}
+\title{Bulk Gene Set Enrichment Analysis (GSEA)}
+\usage{
+arseq.gsea.runall(
+  ranked.list,
+  save = FALSE,
+  custom.gsea = NULL,
+  save.dir = getwd()
+)
+}
+\arguments{
+\item{ranked.list}{Ranked list of genes for GSEA analysis. Use 'arseq.gsea.preprocess' to generate ranked list of genes from DESeq2 differential gene expression analysis.}
+
+\item{save}{Logical. Argument to indicate if to save the results in disk (pdf and csv files). Default=FALSE}
+
+\item{custom.gsea}{User defined gene list to perform GSEA. File need to be supplied as a dataframe with each row as a gene list.}
+
+\item{save.dir}{Directory to save the results when 'save=TRUE'. Default= Working Directory.}
+}
+\value{
+List containing all the GSEA dataframe and ggplot objects.
+}
+\description{
+Performing GSEA enrichment analysis on a ranked list of genes for all msigDB.
+}
+\examples{
+\dontrun{
+ranked.list <- arseq.gsea.preprocess (deg=example_deg)
+gsea.output <- arseq.gsea.runall (ranked.list)
+}
 }
diff --git a/man/arseq.kegg.enrich.Rd b/man/arseq.kegg.enrich.Rd
index ca4b113..739b830 100644
--- a/man/arseq.kegg.enrich.Rd
+++ b/man/arseq.kegg.enrich.Rd
@@ -1,24 +1,24 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.kegg.enrich.R
-\name{arseq.kegg.enrich}
-\alias{arseq.kegg.enrich}
-\title{KEGG pathway enrichment}
-\usage{
-arseq.kegg.enrich(deg, kegg.compare = "as.group")
-}
-\arguments{
-\item{deg}{Differentially expressed genes dataframe returned by DESeq2 analysis}
-
-\item{kegg.compare}{Character, which comparison scheme to be used: 'paired', 'unpaired', '1ongroup', 'as.group'. 'paired' is the default, ref and samp are of equal length and one-on-one paired by the original experimental design; 'as.group', group-on-group comparison between ref and samp; 'unpaired' (used to be '1on1'), one-on-one comparison between all possible ref and samp combinations, although the original experimental design may not be one-on-one paired; '1ongroup', comparison between one samp column at a time vs the average of all ref columns.}
-}
-\value{
-Enrichment dataframe
-}
-\description{
-Performing KEGG pathway enrichment analysis on the significantly differentially expressed genes.
-}
-\examples{
-\dontrun{
-kegg.enrich <- arseq.kegg.enrich (example_deg)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.kegg.enrich.R
+\name{arseq.kegg.enrich}
+\alias{arseq.kegg.enrich}
+\title{KEGG pathway enrichment}
+\usage{
+arseq.kegg.enrich(deg, kegg.compare = "as.group")
+}
+\arguments{
+\item{deg}{Differentially expressed genes dataframe returned by DESeq2 analysis}
+
+\item{kegg.compare}{Character, which comparison scheme to be used: 'paired', 'unpaired', '1ongroup', 'as.group'. 'paired' is the default, ref and samp are of equal length and one-on-one paired by the original experimental design; 'as.group', group-on-group comparison between ref and samp; 'unpaired' (used to be '1on1'), one-on-one comparison between all possible ref and samp combinations, although the original experimental design may not be one-on-one paired; '1ongroup', comparison between one samp column at a time vs the average of all ref columns.}
+}
+\value{
+Enrichment dataframe
+}
+\description{
+Performing KEGG pathway enrichment analysis on the significantly differentially expressed genes.
+}
+\examples{
+\dontrun{
+kegg.enrich <- arseq.kegg.enrich (example_deg)
+}
 }
diff --git a/man/arseq.kegg.enrich.plot.Rd b/man/arseq.kegg.enrich.plot.Rd
index 287609c..f1cc76c 100644
--- a/man/arseq.kegg.enrich.plot.Rd
+++ b/man/arseq.kegg.enrich.plot.Rd
@@ -1,30 +1,34 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.kegg.enrich.plot.R
-\name{arseq.kegg.enrich.plot}
-\alias{arseq.kegg.enrich.plot}
-\title{Gene Ontology (GO) term enrichment}
-\usage{
-arseq.kegg.enrich.plot(kegg.enrich, foldchanges, save.dir = getwd(),
-  pathway.plots = TRUE)
-}
-\arguments{
-\item{kegg.enrich}{Enrichment dataframe. Output of the function 'arseq.kegg.enrich'}
-
-\item{foldchanges}{Foldchange information to overlay on the pathway plots.}
-
-\item{save.dir}{User defined directory to save the plots in. Default is working directory.}
-
-\item{pathway.plots}{Logical.Parameter to indicate if the pathways figures need to be drawn.}
-}
-\value{
-GO enrichment plot
-}
-\description{
-Plotting the top 5 enriched term from each category
-}
-\examples{
-\dontrun{
-kegg.enrich <- arseq.kegg.enrich (example_deg)
-kegg.plot <- arseq.kegg.enrich.plot (kegg.enrich, foldchanges=kegg.enrich$foldchanges)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.kegg.enrich.plot.R
+\name{arseq.kegg.enrich.plot}
+\alias{arseq.kegg.enrich.plot}
+\title{Gene Ontology (GO) term enrichment}
+\usage{
+arseq.kegg.enrich.plot(
+  kegg.enrich,
+  foldchanges,
+  save.dir = getwd(),
+  pathway.plots = TRUE
+)
+}
+\arguments{
+\item{kegg.enrich}{Enrichment dataframe. Output of the function 'arseq.kegg.enrich'}
+
+\item{foldchanges}{Foldchange information to overlay on the pathway plots.}
+
+\item{save.dir}{User defined directory to save the plots in. Default is working directory.}
+
+\item{pathway.plots}{Logical.Parameter to indicate if the pathways figures need to be drawn.}
+}
+\value{
+GO enrichment plot
+}
+\description{
+Plotting the top 5 enriched term from each category
+}
+\examples{
+\dontrun{
+kegg.enrich <- arseq.kegg.enrich (example_deg)
+kegg.plot <- arseq.kegg.enrich.plot (kegg.enrich, foldchanges=kegg.enrich$foldchanges)
+}
 }
diff --git a/man/arseq.kmeans.Rd b/man/arseq.kmeans.Rd
new file mode 100644
index 0000000..98230af
--- /dev/null
+++ b/man/arseq.kmeans.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.kmeans.R
+\name{arseq.kmeans}
+\alias{arseq.kmeans}
+\title{K Means clustering}
+\usage{
+arseq.kmeans(data, kmeans = kmeans)
+}
+\arguments{
+\item{data}{Normalized expression dataframe}
+
+\item{kmeans}{integer: The number of clusters to be returned}
+}
+\value{
+Kmeans clusters
+}
+\description{
+K means clustering to identify gene modules
+}
+\examples{
+clusters <- arseq.kmeans (data, kmeans=10)
+}
diff --git a/man/arseq.kmeans.plot.Rd b/man/arseq.kmeans.plot.Rd
new file mode 100644
index 0000000..4f5b732
--- /dev/null
+++ b/man/arseq.kmeans.plot.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.kmeans.plot.R
+\name{arseq.kmeans.plot}
+\alias{arseq.kmeans.plot}
+\title{K Means clustering Heatmap}
+\usage{
+arseq.kmeans.plot(
+  data,
+  clusters,
+  metadata,
+  intgroup = "arseq.group",
+  save.plot = FALSE,
+  save.dir = getwd()
+)
+}
+\arguments{
+\item{data}{Normalized expression dataframe}
+
+\item{clusters}{List of gene clusters returned by Kmeans clustering algorithm}
+}
+\value{
+Heatmap
+}
+\description{
+Heatmap of the Most Variable genes divided into clusters
+}
+\examples{
+arseq.kmeans.plot (data,clusters=kmeansclusters,metadata= example_meta,intgroup="treatment")
+}
diff --git a/man/arseq.kmeans.reactome.plot.Rd b/man/arseq.kmeans.reactome.plot.Rd
new file mode 100644
index 0000000..0361501
--- /dev/null
+++ b/man/arseq.kmeans.reactome.plot.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.kmeans.reactome.plot.R
+\name{arseq.kmeans.reactome.plot}
+\alias{arseq.kmeans.reactome.plot}
+\title{Reactome Pathway Enrichment of Kmeans clustering output}
+\usage{
+arseq.kmeans.reactome.plot(clusters, save.plot = FALSE, save.dir = getwd())
+}
+\arguments{
+\item{clusters}{List of gene clusters returned by Kmeans clustering algorithm}
+}
+\value{
+DotPlot of Reactome Enrichment
+}
+\description{
+Reactome Pathway Enrichment of Kmeans clustering output
+}
+\examples{
+arseq.kmeans.reactome.plot (clusters)
+}
diff --git a/man/arseq.mds.plot.Rd b/man/arseq.mds.plot.Rd
index 9abf755..4bcc6e6 100644
--- a/man/arseq.mds.plot.Rd
+++ b/man/arseq.mds.plot.Rd
@@ -1,24 +1,24 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.mds.plot.R
-\name{arseq.mds.plot}
-\alias{arseq.mds.plot}
-\title{Multidimensional scaling (MDS) Analysis}
-\usage{
-arseq.mds.plot(dds, intgroup = "arseq.group")
-}
-\arguments{
-\item{dds}{DESeq2 object}
-
-\item{intgroup}{interesting groups: a character vector of names in colData(x) to use for grouping.}
-}
-\value{
-ggplot of the two selected principal components
-}
-\description{
-Plots the Multidimensional scaling (MDS) factors.
-}
-\examples{
-\dontrun{
-mds.plot <- arseq.mds.plot (example_dds, intgroup="treatment")
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.mds.plot.R
+\name{arseq.mds.plot}
+\alias{arseq.mds.plot}
+\title{Multidimensional scaling (MDS) Analysis}
+\usage{
+arseq.mds.plot(dds, intgroup = "arseq.group")
+}
+\arguments{
+\item{dds}{DESeq2 object}
+
+\item{intgroup}{interesting groups: a character vector of names in colData(x) to use for grouping.}
+}
+\value{
+ggplot of the two selected principal components
+}
+\description{
+Plots the Multidimensional scaling (MDS) factors.
+}
+\examples{
+\dontrun{
+mds.plot <- arseq.mds.plot (example_dds, intgroup="treatment")
+}
 }
diff --git a/man/arseq.mvg.Rd b/man/arseq.mvg.Rd
index c5704ac..ed1ed1e 100644
--- a/man/arseq.mvg.Rd
+++ b/man/arseq.mvg.Rd
@@ -1,24 +1,24 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.mvg.R
-\name{arseq.mvg}
-\alias{arseq.mvg}
-\title{Most Variable Genes}
-\usage{
-arseq.mvg(data, variable.genes = 1000, dds.object = TRUE)
-}
-\arguments{
-\item{data}{DESeq2 object or normalized expression dataframe}
-
-\item{variable.genes}{numeric: The number of most variable genes to be identified. By default, the program identifies the top 1000 most variable genes.}
-
-\item{dds.object}{Logical parameter indicating if the data is a DESeq2 object. Default=TRUE}
-}
-\value{
-The most variable genes
-}
-\description{
-Identifying the most variable genes in the dataset
-}
-\examples{
-mvg <- arseq.mvg (example_dds)
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.mvg.R
+\name{arseq.mvg}
+\alias{arseq.mvg}
+\title{Most Variable Genes}
+\usage{
+arseq.mvg(data, variable.genes = variable.genes, dds.object = TRUE)
+}
+\arguments{
+\item{data}{DESeq2 object or normalized expression dataframe}
+
+\item{variable.genes}{numeric: The number of most variable genes to be identified. By default, the program identifies the top 1000 most variable genes.}
+
+\item{dds.object}{Logical parameter indicating if the data is a DESeq2 object. Default=TRUE}
+}
+\value{
+The most variable genes
+}
+\description{
+Identifying the most variable genes in the dataset
+}
+\examples{
+mvg <- arseq.mvg (example_dds)
 }
diff --git a/man/arseq.mvg.plot.Rd b/man/arseq.mvg.plot.Rd
index 545f852..148359c 100644
--- a/man/arseq.mvg.plot.Rd
+++ b/man/arseq.mvg.plot.Rd
@@ -1,30 +1,35 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.mvg.plot.R
-\name{arseq.mvg.plot}
-\alias{arseq.mvg.plot}
-\title{Most Variable Genes}
-\usage{
-arseq.mvg.plot(mvg, metadata, intgroup = "arseq.group",
-  save.plot = FALSE, save.dir = getwd())
-}
-\arguments{
-\item{mvg}{Expression matrix of the most variable genes identified using the function 'arseq.mvg'}
-
-\item{metadata}{A CSV file with information regarding the samples.}
-
-\item{intgroup}{interesting groups: a character vector of names in colData(x) to use for grouping.}
-
-\item{save.plot}{Logical. Argument to state if the plot needs to be saved in disk. Default: FALSE}
-
-\item{save.dir}{Location to save the plot when 'save.plot=TRUE'. Default: Working Directory.}
-}
-\value{
-Heatmap of the most variable genes
-}
-\description{
-Identifying the most variable genes in the dataset
-}
-\examples{
-mvg <- arseq.mvg (example_dds)
-mvg.plot <- arseq.mvg.plot (mvg[1:100,],metadata= example_meta,intgroup="treatment")
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.mvg.plot.R
+\name{arseq.mvg.plot}
+\alias{arseq.mvg.plot}
+\title{Most Variable Genes}
+\usage{
+arseq.mvg.plot(
+  mvg,
+  metadata,
+  intgroup = "arseq.group",
+  save.plot = FALSE,
+  save.dir = getwd()
+)
+}
+\arguments{
+\item{mvg}{Expression matrix of the most variable genes identified using the function 'arseq.mvg'}
+
+\item{metadata}{A CSV file with information regarding the samples.}
+
+\item{intgroup}{interesting groups: a character vector of names in colData(x) to use for grouping.}
+
+\item{save.plot}{Logical. Argument to state if the plot needs to be saved in disk. Default: FALSE}
+
+\item{save.dir}{Location to save the plot when 'save.plot=TRUE'. Default: Working Directory.}
+}
+\value{
+Heatmap of the most variable genes
+}
+\description{
+Identifying the most variable genes in the dataset
+}
+\examples{
+mvg <- arseq.mvg (example_dds)
+mvg.plot <- arseq.mvg.plot (mvg[1:100,],metadata= example_meta,intgroup="treatment")
 }
diff --git a/man/arseq.pca.Rd b/man/arseq.pca.Rd
index d513e31..bb60ec3 100644
--- a/man/arseq.pca.Rd
+++ b/man/arseq.pca.Rd
@@ -1,24 +1,24 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.pca.R
-\name{arseq.pca}
-\alias{arseq.pca}
-\title{Principal Component Analysis}
-\usage{
-arseq.pca(dds, ntop = 500)
-}
-\arguments{
-\item{dds}{DESeq2 object}
-
-\item{ntop}{number of top genes to use for principal components, selected by highest row variance}
-}
-\value{
-Eigen vectors of the Principal components
-}
-\description{
-Plots any two specified principal components. By default it plots the first two principal components.
-}
-\examples{
-\dontrun{
-pca.ev <- arseq.pca (example_dds)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.pca.R
+\name{arseq.pca}
+\alias{arseq.pca}
+\title{Principal Component Analysis}
+\usage{
+arseq.pca(dds, ntop = 500)
+}
+\arguments{
+\item{dds}{DESeq2 object}
+
+\item{ntop}{number of top genes to use for principal components, selected by highest row variance}
+}
+\value{
+Eigen vectors of the Principal components
+}
+\description{
+Plots any two specified principal components. By default it plots the first two principal components.
+}
+\examples{
+\dontrun{
+pca.ev <- arseq.pca (example_dds)
+}
 }
diff --git a/man/arseq.pca.plot.Rd b/man/arseq.pca.plot.Rd
index 7b69c12..816c457 100644
--- a/man/arseq.pca.plot.Rd
+++ b/man/arseq.pca.plot.Rd
@@ -1,33 +1,39 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.pca.plot.R
-\name{arseq.pca.plot}
-\alias{arseq.pca.plot}
-\title{Principal Component Analysis}
-\usage{
-arseq.pca.plot(dds, intgroup = "arseq.group", ntop = 500, pc.a = 1,
-  pc.b = 2, returnData = FALSE)
-}
-\arguments{
-\item{dds}{DESeq2 object}
-
-\item{intgroup}{interesting groups: a character vector of names in colData(x) to use for grouping.}
-
-\item{ntop}{number of top genes to use for principal components, selected by highest row variance}
-
-\item{pc.a}{numeric: Defines the first principal component. Default:1}
-
-\item{pc.b}{numeric: Defines the second principal component.Default:2}
-
-\item{returnData}{should the function only return the data.frame of 'pc.a' and 'pc.b' with intgroup covariates for custom plotting (default is FALSE)}
-}
-\value{
-ggplot of the two selected principal components
-}
-\description{
-Plots any two specified principal components. By default it plots the first two principal components.
-}
-\examples{
-\dontrun{
-pca.plot <- arseq.pca.plot (example_dds, intgroup="treatment")
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.pca.plot.R
+\name{arseq.pca.plot}
+\alias{arseq.pca.plot}
+\title{Principal Component Analysis}
+\usage{
+arseq.pca.plot(
+  dds,
+  intgroup = "arseq.group",
+  ntop = 500,
+  pc.a = 1,
+  pc.b = 2,
+  returnData = FALSE
+)
+}
+\arguments{
+\item{dds}{DESeq2 object}
+
+\item{intgroup}{interesting groups: a character vector of names in colData(x) to use for grouping.}
+
+\item{ntop}{number of top genes to use for principal components, selected by highest row variance}
+
+\item{pc.a}{numeric: Defines the first principal component. Default:1}
+
+\item{pc.b}{numeric: Defines the second principal component.Default:2}
+
+\item{returnData}{should the function only return the data.frame of 'pc.a' and 'pc.b' with intgroup covariates for custom plotting (default is FALSE)}
+}
+\value{
+ggplot of the two selected principal components
+}
+\description{
+Plots any two specified principal components. By default it plots the first two principal components.
+}
+\examples{
+\dontrun{
+pca.plot <- arseq.pca.plot (example_dds, intgroup="treatment")
+}
 }
diff --git a/man/arseq.pheatmap.Rd b/man/arseq.pheatmap.Rd
index fa39677..e5f0c36 100644
--- a/man/arseq.pheatmap.Rd
+++ b/man/arseq.pheatmap.Rd
@@ -1,26 +1,25 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.pheatmap.R
-\name{arseq.pheatmap}
-\alias{arseq.pheatmap}
-\title{Pheatmap plotting function}
-\usage{
-arseq.pheatmap(x, filename, width = 7, height = 7,
-  save.dir = getwd())
-}
-\arguments{
-\item{x}{Expression matrix or any numeric matrix to be visualized as a heatmap.}
-
-\item{filename}{The pdf file name.}
-
-\item{width}{Width of the pdf file.}
-
-\item{height}{Height of the pdf file.}
-
-\item{save.dir}{Location to save the heatmap}
-}
-\value{
-Does not return anything. The function saves a pdf file to the working directory.
-}
-\description{
-The function saves the pheatmap as a pdf.
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.pheatmap.R
+\name{arseq.pheatmap}
+\alias{arseq.pheatmap}
+\title{Pheatmap plotting function}
+\usage{
+arseq.pheatmap(x, filename, width = 7, height = 7, save.dir = getwd())
+}
+\arguments{
+\item{x}{Expression matrix or any numeric matrix to be visualized as a heatmap.}
+
+\item{filename}{The pdf file name.}
+
+\item{width}{Width of the pdf file.}
+
+\item{height}{Height of the pdf file.}
+
+\item{save.dir}{Location to save the heatmap}
+}
+\value{
+Does not return anything. The function saves a pdf file to the working directory.
+}
+\description{
+The function saves the pheatmap as a pdf.
 }
diff --git a/man/arseq.plot.save.Rd b/man/arseq.plot.save.Rd
index 570ae6a..21dc63f 100644
--- a/man/arseq.plot.save.Rd
+++ b/man/arseq.plot.save.Rd
@@ -1,26 +1,31 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.plot.save.R
-\name{arseq.plot.save}
-\alias{arseq.plot.save}
-\title{Save plots}
-\usage{
-arseq.plot.save(arseq.plot, filename, width = 7, height = 7,
-  save.dir = getwd())
-}
-\arguments{
-\item{arseq.plot}{The plot to be saved}
-
-\item{filename}{The pdf file name.}
-
-\item{width}{Width of the pdf file.}
-
-\item{height}{Height of the pdf file.}
-
-\item{save.dir}{Location to save the plot}
-}
-\value{
-Does not return an object. Function saves plots in directory
-}
-\description{
-Function to save plots as a pdf file in user defined directory
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.plot.save.R
+\name{arseq.plot.save}
+\alias{arseq.plot.save}
+\title{Save plots}
+\usage{
+arseq.plot.save(
+  arseq.plot,
+  filename,
+  width = 7,
+  height = 7,
+  save.dir = getwd()
+)
+}
+\arguments{
+\item{arseq.plot}{The plot to be saved}
+
+\item{filename}{The pdf file name.}
+
+\item{width}{Width of the pdf file.}
+
+\item{height}{Height of the pdf file.}
+
+\item{save.dir}{Location to save the plot}
+}
+\value{
+Does not return an object. Function saves plots in directory
+}
+\description{
+Function to save plots as a pdf file in user defined directory
 }
diff --git a/man/arseq.poisd.dist.Rd b/man/arseq.poisd.dist.Rd
index d658980..1a0d494 100644
--- a/man/arseq.poisd.dist.Rd
+++ b/man/arseq.poisd.dist.Rd
@@ -1,20 +1,20 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.poisd.dist.R
-\name{arseq.poisd.dist}
-\alias{arseq.poisd.dist}
-\title{Poisson distance}
-\usage{
-arseq.poisd.dist(dds)
-}
-\arguments{
-\item{dds}{DESeq2 object}
-}
-\value{
-Poisson distance matrix
-}
-\description{
-Calculate the Poisson distance between samples.
-}
-\examples{
-poisd.dist <- arseq.poisd.dist (example_dds)
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.poisd.dist.R
+\name{arseq.poisd.dist}
+\alias{arseq.poisd.dist}
+\title{Poisson distance}
+\usage{
+arseq.poisd.dist(dds)
+}
+\arguments{
+\item{dds}{DESeq2 object}
+}
+\value{
+Poisson distance matrix
+}
+\description{
+Calculate the Poisson distance between samples.
+}
+\examples{
+poisd.dist <- arseq.poisd.dist (example_dds)
 }
diff --git a/man/arseq.poisd.dist.plot.Rd b/man/arseq.poisd.dist.plot.Rd
index 8f711bb..fc625a6 100644
--- a/man/arseq.poisd.dist.plot.Rd
+++ b/man/arseq.poisd.dist.plot.Rd
@@ -1,21 +1,21 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.poisd.dist.plot.R
-\name{arseq.poisd.dist.plot}
-\alias{arseq.poisd.dist.plot}
-\title{Poisson distance heatmap}
-\usage{
-arseq.poisd.dist.plot(poisd.dist)
-}
-\arguments{
-\item{poisd.dist}{Poisson distance matrix.}
-}
-\value{
-Poisson distance heatmap.
-}
-\description{
-Plots a heatmap of the Poisson distance between samples using pheatmap.
-}
-\examples{
-poisd.dist <- arseq.poisd.dist (example_dds)
-poisd.plot <- arseq.poisd.dist.plot (poisd.dist)
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.poisd.dist.plot.R
+\name{arseq.poisd.dist.plot}
+\alias{arseq.poisd.dist.plot}
+\title{Poisson distance heatmap}
+\usage{
+arseq.poisd.dist.plot(poisd.dist)
+}
+\arguments{
+\item{poisd.dist}{Poisson distance matrix.}
+}
+\value{
+Poisson distance heatmap.
+}
+\description{
+Plots a heatmap of the Poisson distance between samples using pheatmap.
+}
+\examples{
+poisd.dist <- arseq.poisd.dist (example_dds)
+poisd.plot <- arseq.poisd.dist.plot (poisd.dist)
 }
diff --git a/man/arseq.reactome.enrich.Rd b/man/arseq.reactome.enrich.Rd
new file mode 100644
index 0000000..b8e4ac1
--- /dev/null
+++ b/man/arseq.reactome.enrich.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.reactome.enrich.R
+\name{arseq.reactome.enrich}
+\alias{arseq.reactome.enrich}
+\title{Reactome enrichment Analysis}
+\usage{
+arseq.reactome.enrich(
+  deg,
+  Padj = 0.05,
+  plot = FALSE,
+  save.plot = FALSE,
+  save.dir = getwd()
+)
+}
+\arguments{
+\item{deg}{Differentially expressed genes dataframe returned by DESeq2 analysis}
+
+\item{Padj}{Numeric. Adjusted P Value cut off to define the differentially expressed genes. Default = 0.05}
+}
+\value{
+Enrichment dataframe
+}
+\description{
+Performing reactome enrichment analysis on the significantly differentially expressed genes.
+}
+\examples{
+\dontrun{
+reactome.enrich <- arseq.go.enrich (example_deg)
+}
+}
diff --git a/man/arseq.volcano.plot.Rd b/man/arseq.volcano.plot.Rd
index 509f21e..1d93e7d 100644
--- a/man/arseq.volcano.plot.Rd
+++ b/man/arseq.volcano.plot.Rd
@@ -1,24 +1,24 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arseq.volcano.plot.R
-\name{arseq.volcano.plot}
-\alias{arseq.volcano.plot}
-\title{Volcano Plot}
-\usage{
-arseq.volcano.plot(deg, pCutoff = 0.01)
-}
-\arguments{
-\item{deg}{Differentially expressed genes returned by DESeq2 analysis}
-
-\item{pCutoff}{Cut-off for statistical significance. A horizontal line will be drawn at -log10(pCutoff). DEFAULT = 0.01. OPTIONAL.}
-}
-\value{
-Volcano plot
-}
-\description{
-Volcano plot of the differentially expressed genes.
-}
-\examples{
-\dontrun{
-volcano.plot <- arseq.volcano.plot (example_deg)
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/arseq.volcano.plot.R
+\name{arseq.volcano.plot}
+\alias{arseq.volcano.plot}
+\title{Volcano Plot}
+\usage{
+arseq.volcano.plot(deg, pCutoff = 0.01)
+}
+\arguments{
+\item{deg}{Differentially expressed genes returned by DESeq2 analysis}
+
+\item{pCutoff}{Cut-off for statistical significance. A horizontal line will be drawn at -log10(pCutoff). DEFAULT = 0.01. OPTIONAL.}
+}
+\value{
+Volcano plot
+}
+\description{
+Volcano plot of the differentially expressed genes.
+}
+\examples{
+\dontrun{
+volcano.plot <- arseq.volcano.plot (example_deg)
+}
 }
diff --git a/man/bods.Rd b/man/bods.Rd
index e82dc1a..7522456 100644
--- a/man/bods.Rd
+++ b/man/bods.Rd
@@ -1,13 +1,13 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/bods.R
-\docType{data}
-\name{bods}
-\alias{bods}
-\title{bods}
-\format{dataframe}
-\usage{
-bods
-}
-\description{
-The various organisms pathview package supports.
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bods.R
+\docType{data}
+\name{bods}
+\alias{bods}
+\title{bods}
+\format{dataframe}
+\usage{
+bods
+}
+\description{
+The various organisms pathview package supports.
 }
diff --git a/man/dot-onAttach.Rd b/man/dot-onAttach.Rd
index 31cc406..545a446 100644
--- a/man/dot-onAttach.Rd
+++ b/man/dot-onAttach.Rd
@@ -1,16 +1,16 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/startup.R
-\name{.onAttach}
-\alias{.onAttach}
-\title{Startup Message}
-\usage{
-.onAttach(libname, pkgname)
-}
-\arguments{
-\item{libname}{Library Name}
-
-\item{pkgname}{Package name}
-}
-\description{
-ARSeq- An automated RNASeq analysis pipeline
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/startup.R
+\name{.onAttach}
+\alias{.onAttach}
+\title{Startup Message}
+\usage{
+.onAttach(libname, pkgname)
+}
+\arguments{
+\item{libname}{Library Name}
+
+\item{pkgname}{Package name}
+}
+\description{
+ARSeq- An automated RNASeq analysis pipeline
 }
diff --git a/man/example_data.Rd b/man/example_data.Rd
index b6131d7..eae052d 100644
--- a/man/example_data.Rd
+++ b/man/example_data.Rd
@@ -1,14 +1,14 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/example_data.R
-\docType{data}
-\name{example_data}
-\alias{example_data}
-\title{Counts table}
-\format{dataframe}
-\usage{
-example_data
-}
-\description{
-Example counts table.
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/example_data.R
+\docType{data}
+\name{example_data}
+\alias{example_data}
+\title{Counts table}
+\format{dataframe}
+\usage{
+example_data
+}
+\description{
+Example counts table.
+}
 \keyword{datasets}
diff --git a/man/example_dds.Rd b/man/example_dds.Rd
index 59f396d..9413a7c 100644
--- a/man/example_dds.Rd
+++ b/man/example_dds.Rd
@@ -1,14 +1,14 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/example_dds.R
-\docType{data}
-\name{example_dds}
-\alias{example_dds}
-\title{DESeq2 object}
-\format{object}
-\usage{
-example_dds
-}
-\description{
-DESeq2 object of the example_data
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/example_dds.R
+\docType{data}
+\name{example_dds}
+\alias{example_dds}
+\title{DESeq2 object}
+\format{object}
+\usage{
+example_dds
+}
+\description{
+DESeq2 object of the example_data
+}
 \keyword{datasets}
diff --git a/man/example_deg.Rd b/man/example_deg.Rd
index 2cf434c..90a70c6 100644
--- a/man/example_deg.Rd
+++ b/man/example_deg.Rd
@@ -1,14 +1,14 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/example_deg.R
-\docType{data}
-\name{example_deg}
-\alias{example_deg}
-\title{Differentially expressed genes}
-\format{dataframe}
-\usage{
-example_deg
-}
-\description{
-Example Differentially expressed genes dataframe
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/example_deg.R
+\docType{data}
+\name{example_deg}
+\alias{example_deg}
+\title{Differentially expressed genes}
+\format{dataframe}
+\usage{
+example_deg
+}
+\description{
+Example Differentially expressed genes dataframe
+}
 \keyword{datasets}
diff --git a/man/example_meta.Rd b/man/example_meta.Rd
index d0a4a91..3463f77 100644
--- a/man/example_meta.Rd
+++ b/man/example_meta.Rd
@@ -1,13 +1,13 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/example_meta.R
-\docType{data}
-\name{example_meta}
-\alias{example_meta}
-\title{Meta data}
-\format{dataframe}
-\usage{
-example_meta
-}
-\description{
-Example meta data file. Follow this structure to make your own meta data file. Please note that the order of the samples and their names need to be exactly same as that of the counts table.
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/example_meta.R
+\docType{data}
+\name{example_meta}
+\alias{example_meta}
+\title{Meta data}
+\format{dataframe}
+\usage{
+example_meta
+}
+\description{
+Example meta data file. Follow this structure to make your own meta data file. Please note that the order of the samples and their names need to be exactly same as that of the counts table.
 }
diff --git a/man/g_variables.Rd b/man/g_variables.Rd
index d4ae59a..d1de8be 100644
--- a/man/g_variables.Rd
+++ b/man/g_variables.Rd
@@ -1,10 +1,9 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/globals.R
-\docType{package}
-\name{g_variables}
-\alias{g_variables}
-\alias{g_variables-package}
-\title{Global variables}
-\description{
-Global variables
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/globals.R
+\docType{package}
+\name{g_variables}
+\alias{g_variables}
+\title{Global variables}
+\description{
+Global variables
 }
diff --git a/man/kegg.sets.hs.Rd b/man/kegg.sets.hs.Rd
index 4a0aa6d..ff11857 100644
--- a/man/kegg.sets.hs.Rd
+++ b/man/kegg.sets.hs.Rd
@@ -1,13 +1,13 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/kegg.sets.hs.R
-\docType{data}
-\name{kegg.sets.hs}
-\alias{kegg.sets.hs}
-\title{kegg.sets.hs}
-\usage{
-kegg.sets.hs
-}
-\description{
-Kegg pathway gene sets.
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kegg.sets.hs.R
+\docType{data}
+\name{kegg.sets.hs}
+\alias{kegg.sets.hs}
+\title{kegg.sets.hs}
+\usage{
+kegg.sets.hs
+}
+\description{
+Kegg pathway gene sets.
+}
 \keyword{datasets}
diff --git a/man/my_plots.Rd b/man/my_plots.Rd
index da52930..ddb7289 100644
--- a/man/my_plots.Rd
+++ b/man/my_plots.Rd
@@ -1,13 +1,13 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/my_plots.R
-\docType{data}
-\name{my_plots}
-\alias{my_plots}
-\title{my_plots}
-\format{dataframe}
-\usage{
-my_plots
-}
-\description{
-An empty plot list to intialize the plotting parameters
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/my_plots.R
+\docType{data}
+\name{my_plots}
+\alias{my_plots}
+\title{my_plots}
+\format{dataframe}
+\usage{
+my_plots
+}
+\description{
+An empty plot list to intialize the plotting parameters
 }