diff --git a/DESCRIPTION b/DESCRIPTION
index f0601f5..45752e9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: vite
 Type: Package
 Title: Analyzing single-cell data using graphs
-Version: 0.4.7
+Version: 0.4.8
 Authors@R: "Pier Federico Gherardini <pfgherardini@parkerici.org> [aut, cre]"
 Description: This is a package for visualization and analysis of high-dimensional
     single-cell data using graphs
@@ -13,4 +13,4 @@ LinkingTo: Rcpp
 License: GPL v3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.0
+RoxygenNote: 7.1.1
diff --git a/NAMESPACE b/NAMESPACE
index 4bf6050..ec75c80 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,8 @@
 
 export(build_graph)
 export(complete_forceatlas2)
+export(cosine_similarity_from_matrix)
+export(cosine_similarity_matrix)
 export(filter_matrix_by_rank)
 export(get_scaffold_map)
 export(get_unsupervised_graph)
diff --git a/R/unsupervised.R b/R/unsupervised.R
index f8b7ae7..7f9d23e 100644
--- a/R/unsupervised.R
+++ b/R/unsupervised.R
@@ -6,6 +6,7 @@
 #' @return Returns a vector of length \code{N} containing the cosine similarity between
 #'   the vector \code{x} and all the rows of \code{m}
 #'
+#' @export
 cosine_similarity_from_matrix <- function(x, m) {
     x <- x / as.vector(sqrt(crossprod(x)))
     return(as.vector((m %*% x) / sqrt(rowSums(m^2))))
@@ -21,6 +22,8 @@ cosine_similarity_from_matrix <- function(x, m) {
 #'
 #' @return Returns an \code{N x N} matrix with the cosine similarity between the corresponding rows in \code{m}
 #'
+#'
+#' @export
 cosine_similarity_matrix <- function(m){
     ret <- m %*% t(m) / (sqrt(rowSums(m^2) %*% t(rowSums(m^2))))
     return(ret)
diff --git a/man/add_vertices_to_landmarks_graph.Rd b/man/add_vertices_to_landmarks_graph.Rd
index 2416c6e..7347175 100644
--- a/man/add_vertices_to_landmarks_graph.Rd
+++ b/man/add_vertices_to_landmarks_graph.Rd
@@ -4,8 +4,13 @@
 \alias{add_vertices_to_landmarks_graph}
 \title{Add cluster vertices to a landmark graph}
 \usage{
-add_vertices_to_landmarks_graph(G, tab.clustered, tab.landmarks, col.names,
-  min.similarity = 0.5)
+add_vertices_to_landmarks_graph(
+  G,
+  tab.clustered,
+  tab.landmarks,
+  col.names,
+  min.similarity = 0.5
+)
 }
 \arguments{
 \item{G}{An \code{igraph} object representing the landmark graph}
diff --git a/man/complete_forceatlas2.Rd b/man/complete_forceatlas2.Rd
index 809f855..ad9ec79 100644
--- a/man/complete_forceatlas2.Rd
+++ b/man/complete_forceatlas2.Rd
@@ -4,8 +4,13 @@
 \alias{complete_forceatlas2}
 \title{Performs a Complete cycle of ForceAtlas2}
 \usage{
-complete_forceatlas2(G, first.iter = 1000, overlap.method = NULL,
-  overlap.iter = NULL, ...)
+complete_forceatlas2(
+  G,
+  first.iter = 1000,
+  overlap.method = NULL,
+  overlap.iter = NULL,
+  ...
+)
 }
 \arguments{
 \item{G}{The input graph}
diff --git a/man/get_distances_from_landmarks.Rd b/man/get_distances_from_landmarks.Rd
index 3db4b7d..92da965 100644
--- a/man/get_distances_from_landmarks.Rd
+++ b/man/get_distances_from_landmarks.Rd
@@ -4,8 +4,7 @@
 \alias{get_distances_from_landmarks}
 \title{Calculate (and filter) disatances between cluster and landmark ondes}
 \usage{
-get_distances_from_landmarks(m, tab, col.names, q.thresh,
-  min.similarity = 0.5)
+get_distances_from_landmarks(m, tab, col.names, q.thresh, min.similarity = 0.5)
 }
 \arguments{
 \item{m}{A \code{data.frame} containing expression values for the cluster nodes}
diff --git a/man/get_scaffold_map.Rd b/man/get_scaffold_map.Rd
index eaa5412..ec9f73e 100644
--- a/man/get_scaffold_map.Rd
+++ b/man/get_scaffold_map.Rd
@@ -4,10 +4,17 @@
 \alias{get_scaffold_map}
 \title{Creates a Scaffold map}
 \usage{
-get_scaffold_map(tab.clustered, col.names, tab.landmarks,
-  G.landmarks = NULL, ew.influence = ceiling(length(col.names)/3),
-  min.similarity = 0.5, inter.cluster.col.names = col.names,
-  inter.cluster.weight.factor = 0.7, overlap.method = "repel")
+get_scaffold_map(
+  tab.clustered,
+  col.names,
+  tab.landmarks,
+  G.landmarks = NULL,
+  ew.influence = ceiling(length(col.names)/3),
+  min.similarity = 0.5,
+  inter.cluster.col.names = col.names,
+  inter.cluster.weight.factor = 0.7,
+  overlap.method = "repel"
+)
 }
 \arguments{
 \item{tab.clustered}{A \code{data.frame} containing the clusters to be represented in the Scaffold map. Each
diff --git a/man/get_unsupervised_graph_from_files.Rd b/man/get_unsupervised_graph_from_files.Rd
index 5f2f926..0b5d77e 100644
--- a/man/get_unsupervised_graph_from_files.Rd
+++ b/man/get_unsupervised_graph_from_files.Rd
@@ -4,11 +4,17 @@
 \alias{get_unsupervised_graph_from_files}
 \title{Builds an unsupervised graph starting from a list of input files}
 \usage{
-get_unsupervised_graph_from_files(files.list, col.names,
-  filtering.threshold, metadata.tab = NULL,
-  metadata.filename.col = NULL, use.basename = TRUE,
-  process.clusters.data = TRUE, clusters.data.out.dir = "./",
-  downsample.to = 1000)
+get_unsupervised_graph_from_files(
+  files.list,
+  col.names,
+  filtering.threshold,
+  metadata.tab = NULL,
+  metadata.filename.col = NULL,
+  use.basename = TRUE,
+  process.clusters.data = TRUE,
+  clusters.data.out.dir = "./",
+  downsample.to = 1000
+)
 }
 \arguments{
 \item{files.list}{The list of files to process. The function will first determine the set of columns that are common to all
diff --git a/man/layout_forceatlas2.Rd b/man/layout_forceatlas2.Rd
index ac4a402..3bc4ab1 100644
--- a/man/layout_forceatlas2.Rd
+++ b/man/layout_forceatlas2.Rd
@@ -4,9 +4,16 @@
 \alias{layout_forceatlas2}
 \title{ForceAtlas2 force-directed layout}
 \usage{
-layout_forceatlas2(G, ew.influence = 1, kgrav = 1, iter = 1000,
-  prevent.overlap = FALSE, fixed = NULL, stopping.tolerance = 0.001,
-  barnes.hut = FALSE)
+layout_forceatlas2(
+  G,
+  ew.influence = 1,
+  kgrav = 1,
+  iter = 1000,
+  prevent.overlap = FALSE,
+  fixed = NULL,
+  stopping.tolerance = 0.001,
+  barnes.hut = FALSE
+)
 }
 \arguments{
 \item{G}{The input \code{igraph} object. The graph must have an edge attribute named \code{weight}, representing edge weights}
diff --git a/man/load_landmarks_from_dir.Rd b/man/load_landmarks_from_dir.Rd
index 0f3c47c..27bc71c 100644
--- a/man/load_landmarks_from_dir.Rd
+++ b/man/load_landmarks_from_dir.Rd
@@ -9,11 +9,12 @@ load_landmarks_from_dir(dir, ...)
 \arguments{
 \item{dir}{A directory name. All the FCS files in the directory will be loaded}
 
-\item{...}{Arguments passed on to \code{load_landmarks}
-\describe{
-  \item{asinh.cofactor}{The cofactor to use for \code{asinh} transformation. If this is \code{NULL} no transformation
+\item{...}{
+  Arguments passed on to \code{\link[=load_landmarks]{load_landmarks}}
+  \describe{
+    \item{\code{asinh.cofactor}}{The cofactor to use for \code{asinh} transformation. If this is \code{NULL} no transformation
 is applied}
-}}
+  }}
 }
 \value{
 Returns a list with the following elements:
diff --git a/man/run_scaffold_analysis.Rd b/man/run_scaffold_analysis.Rd
index a591a2f..075c917 100644
--- a/man/run_scaffold_analysis.Rd
+++ b/man/run_scaffold_analysis.Rd
@@ -4,9 +4,16 @@
 \alias{run_scaffold_analysis}
 \title{High level wrapper for performing a Scaffold analysis}
 \usage{
-run_scaffold_analysis(files.list, ref.file, landmarks.data, col.names,
-  out.dir = "scaffold_result", process.clusters.data = TRUE,
-  downsample.to = 1000, ...)
+run_scaffold_analysis(
+  files.list,
+  ref.file,
+  landmarks.data,
+  col.names,
+  out.dir = "scaffold_result",
+  process.clusters.data = TRUE,
+  downsample.to = 1000,
+  ...
+)
 }
 \arguments{
 \item{files.list}{Character vector. The list of files to process}
diff --git a/man/write_clusters_data.Rd b/man/write_clusters_data.Rd
index 67bccfd..de71b92 100644
--- a/man/write_clusters_data.Rd
+++ b/man/write_clusters_data.Rd
@@ -4,8 +4,12 @@
 \alias{write_clusters_data}
 \title{Write clustering output}
 \usage{
-write_clusters_data(clustered.data, base.name, output.dir = "./",
-  pooled.only = FALSE)
+write_clusters_data(
+  clustered.data,
+  base.name,
+  output.dir = "./",
+  pooled.only = FALSE
+)
 }
 \arguments{
 \item{clustered.data}{A \code{data.frame} containing the clustered data. Each row corresponds to cell. The \code{data.frame}
diff --git a/man/write_scaffold_output.Rd b/man/write_scaffold_output.Rd
index 681fd14..2dc968c 100644
--- a/man/write_scaffold_output.Rd
+++ b/man/write_scaffold_output.Rd
@@ -4,8 +4,14 @@
 \alias{write_scaffold_output}
 \title{Write the result of a Scaffold analysis}
 \usage{
-write_scaffold_output(G, out.dir, out.name, clusters.data = NULL,
-  landmarks.data = NULL, downsample.to = 1000)
+write_scaffold_output(
+  G,
+  out.dir,
+  out.name,
+  clusters.data = NULL,
+  landmarks.data = NULL,
+  downsample.to = 1000
+)
 }
 \arguments{
 \item{G}{An \code{igraph} object representing the Scaffold map}