diff --git a/DESCRIPTION b/DESCRIPTION
index 24d7a3d..6ecd4ab 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -73,5 +73,5 @@ Suggests:
     knitr
 License: GPL (>=2)
 LazyData: TRUE
-RoxygenNote: 5.0.1
+RoxygenNote: 6.1.1
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index 546b437..38b2a72 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(cal_entropy)
 export(centroid_classify)
 export(clean_iterNMF)
 export(clust_by_hier)
+export(clust_silhouette)
 export(comp_module_genelist)
 export(compare_group)
 export(compare_groups_stats)
@@ -30,6 +31,7 @@ export(featureUI)
 export(gene_convert_human_to_mouse)
 export(gene_convert_mouse_to_human)
 export(get_ClaNC_group)
+export(getcentroid)
 export(heatmap.3)
 export(is.whole)
 export(iter_nmf)
@@ -59,6 +61,7 @@ export(nmfres)
 export(nmfresUI)
 export(norm_factors)
 export(parse_tsne_res)
+export(plot_cor_subiNMF)
 export(plot_gene_expression)
 export(plot_modules)
 export(plot_tsne)
diff --git a/man/NetConnectivity.Rd b/man/NetConnectivity.Rd
index 7e246fb..ffcbf89 100644
--- a/man/NetConnectivity.Rd
+++ b/man/NetConnectivity.Rd
@@ -24,4 +24,3 @@ NetConnectivity(mtcars, tao=0.5)
 \keyword{co-expression,}
 \keyword{connectivity}
 \keyword{network,}
-
diff --git a/man/RPM.Rd b/man/RPM.Rd
deleted file mode 100644
index c8409bc..0000000
--- a/man/RPM.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_utils.R
-\name{rpm}
-\alias{rpm}
-\title{Transform the countdata into Reads per million reads}
-\usage{
-rpm(data, mapped_reads)
-}
-\arguments{
-\item{data}{countdata}
-
-\item{mapped_reads}{mapped reads in each library}
-}
-\description{
-Transform the countdata into Reads per million reads
-}
-\examples{
-rpm(data)
-}
-\keyword{RPM}
-
diff --git a/man/UQ.Rd b/man/UQ.Rd
deleted file mode 100644
index 50e9c1d..0000000
--- a/man/UQ.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_utils.R
-\name{uq}
-\alias{uq}
-\title{Transform the countdata by upper quantile value from each sample}
-\usage{
-uq(data, remove.zero = T)
-}
-\arguments{
-\item{data}{countdata}
-}
-\description{
-Upper quartile normalization, add option to remove all zeros in the sample first
-}
-\examples{
-uq(mtcars)
-}
-\keyword{UQ,}
-\keyword{normalization}
-\keyword{quantile,}
-
diff --git a/man/Usoskin.Rd b/man/Usoskin.Rd
index 2908ca8..f4fb756 100644
--- a/man/Usoskin.Rd
+++ b/man/Usoskin.Rd
@@ -38,4 +38,3 @@ catalog illustrates the diversity of sensory types and the cellular complexity u
 somatic sensation.
 }
 \keyword{datasets}
-
diff --git a/man/affy_probe_to_gene_symbol.Rd b/man/affy_probe_to_gene_symbol.Rd
index 8f7b994..6cb927c 100644
--- a/man/affy_probe_to_gene_symbol.Rd
+++ b/man/affy_probe_to_gene_symbol.Rd
@@ -16,4 +16,3 @@ Conversion between affy probe_ID to gene_symbol
 affy_probe_to_gene_symbol("TP53")
 }
 \keyword{standardize}
-
diff --git a/man/assign_label_cex.Rd b/man/assign_label_cex.Rd
index 9528a13..f69d8c8 100644
--- a/man/assign_label_cex.Rd
+++ b/man/assign_label_cex.Rd
@@ -16,4 +16,3 @@ This function allows you to express your love of cats.
 assign_label_cex(100)
 }
 \keyword{cats}
-
diff --git a/man/cal_entropy.Rd b/man/cal_entropy.Rd
index dd43383..0118d3d 100644
--- a/man/cal_entropy.Rd
+++ b/man/cal_entropy.Rd
@@ -9,4 +9,3 @@ cal_entropy(x, base = exp(1))
 \description{
 calculate entroyp
 }
-
diff --git a/man/centroid_classify.Rd b/man/centroid_classify.Rd
index c7743f0..37fc2f0 100644
--- a/man/centroid_classify.Rd
+++ b/man/centroid_classify.Rd
@@ -17,4 +17,3 @@ cat_function()
 }
 \keyword{centroids}
 \keyword{classify}
-
diff --git a/man/clean_iterNMF.Rd b/man/clean_iterNMF.Rd
index e90c81e..931b50b 100644
--- a/man/clean_iterNMF.Rd
+++ b/man/clean_iterNMF.Rd
@@ -4,8 +4,9 @@
 \alias{clean_iterNMF}
 \title{Extract, cleanup, and merge iter_NMF results}
 \usage{
-clean_iterNMF(inmf_res, rawdata, cor.method = "spearman", cor.thresh = 0.9,
-  ctriod.topN = 5000, ctroid.math = "mean", return.all = FALSE)
+clean_iterNMF(inmf_res, rawdata, cor.method = "spearman",
+  cor.thresh = 0.9, ctriod.topN = 5000, ctroid.math = "mean",
+  return.all = FALSE)
 }
 \arguments{
 \item{rawdata}{gene count table for calculating centroids based on the clustering results}
@@ -28,4 +29,3 @@ clean_iterNMF(inmf_res, rawdata)
 }
 \keyword{NMF}
 \keyword{iterative}
-
diff --git a/man/clust_by_hier.Rd b/man/clust_by_hier.Rd
index e93692c..1ed8cd5 100644
--- a/man/clust_by_hier.Rd
+++ b/man/clust_by_hier.Rd
@@ -16,4 +16,3 @@ Clustering by hierarchical
 my.write.matrix(data)
 }
 \keyword{write.matrix}
-
diff --git a/man/clust_silhouette.Rd b/man/clust_silhouette.Rd
new file mode 100644
index 0000000..e997bab
--- /dev/null
+++ b/man/clust_silhouette.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/nmf_utils.R
+\name{clust_silhouette}
+\alias{clust_silhouette}
+\title{Calculate silhouette index between two data frame}
+\usage{
+clust_silhouette(clust1, clust2, method = "euclidean")
+}
+\arguments{
+\item{clust1}{data in cluster1}
+
+\item{clust2}{data in cluster2}
+
+\item{method}{method for calculating distance metrics}
+}
+\description{
+Calculate silhouette index between two data frame
+}
+\keyword{NMF}
+\keyword{iterative}
+\keyword{silhouette}
diff --git a/man/comp_module_genelist.Rd b/man/comp_module_genelist.Rd
index 764118c..62aa4a8 100644
--- a/man/comp_module_genelist.Rd
+++ b/man/comp_module_genelist.Rd
@@ -20,4 +20,3 @@ comp_module_genelist(final_comp_genelist, folderName0="folder")
 \keyword{co-expression,}
 \keyword{connectivity}
 \keyword{network,}
-
diff --git a/man/compare_group.Rd b/man/compare_group.Rd
index 5606888..ef1e27c 100644
--- a/man/compare_group.Rd
+++ b/man/compare_group.Rd
@@ -4,9 +4,9 @@
 \alias{compare_group}
 \title{Compare two groups assignment results}
 \usage{
-compare_group(group1, group2, file.prefix = "Compare.group", title = "",
-  plot = T, save.image = F, add.legend = T, label.size = 5,
-  title.size = 36, angle = 45)
+compare_group(group1, group2, file.prefix = "Compare.group",
+  title = "", plot = T, save.image = F, add.legend = T,
+  label.size = 5, title.size = 36, angle = 45)
 }
 \arguments{
 \item{group1}{vector of clustering 1}
@@ -20,4 +20,3 @@ This function allows you to express your love of cats.
 cat_function()
 }
 \keyword{compare}
-
diff --git a/man/compare_groups_stats.Rd b/man/compare_groups_stats.Rd
index 65df4af..e578835 100644
--- a/man/compare_groups_stats.Rd
+++ b/man/compare_groups_stats.Rd
@@ -15,4 +15,3 @@ compare_groups_stats(x, y, method = "rand", base = exp(1), beta = 1)
 Calculate statistics comparing two clustering results
 }
 \keyword{compare}
-
diff --git a/man/connect_gap_modules.Rd b/man/connect_gap_modules.Rd
index aca2730..fae51c0 100644
--- a/man/connect_gap_modules.Rd
+++ b/man/connect_gap_modules.Rd
@@ -22,4 +22,3 @@ connect_gap_modules(final_summary, final_genelist, allow.gap=1)
 \keyword{co-expression,}
 \keyword{connectivity}
 \keyword{network,}
-
diff --git a/man/corModuleUI.Rd b/man/corModuleUI.Rd
index 89cf524..595c0a8 100644
--- a/man/corModuleUI.Rd
+++ b/man/corModuleUI.Rd
@@ -9,4 +9,3 @@ corModuleUI(id)
 \description{
 Sample correlation plot
 }
-
diff --git a/man/cor_mtest.Rd b/man/cor_mtest.Rd
index 93f8424..3d61728 100644
--- a/man/cor_mtest.Rd
+++ b/man/cor_mtest.Rd
@@ -18,4 +18,3 @@ Load predefined gene list files for heatmap (clustering) result
 cor_mtest("data", ".txt")
 }
 \keyword{lodad}
-
diff --git a/man/create.brewer.color.Rd b/man/create.brewer.color.Rd
index 2919bee..5bd6d80 100644
--- a/man/create.brewer.color.Rd
+++ b/man/create.brewer.color.Rd
@@ -16,4 +16,3 @@ This function allows you to express your love of cats.
 create.brewer.color()
 }
 \keyword{cats}
-
diff --git a/man/create.manual.color.Rd b/man/create.manual.color.Rd
index 8e7d3f2..2830198 100644
--- a/man/create.manual.color.Rd
+++ b/man/create.manual.color.Rd
@@ -19,4 +19,3 @@ create.manual.color(c(1,2,3,1,2,3,2,3), c("red", "blue", "green"))
 }
 \keyword{color}
 \keyword{manual}
-
diff --git a/man/create_centroid.Rd b/man/create_centroid.Rd
index 61014c1..ce2ae1c 100644
--- a/man/create_centroid.Rd
+++ b/man/create_centroid.Rd
@@ -19,4 +19,3 @@ create_centroid(mtcars)
 }
 \keyword{centroid}
 \keyword{reshape}
-
diff --git a/man/def_net_module2.Rd b/man/def_net_module2.Rd
index 790e6ea..12880de 100644
--- a/man/def_net_module2.Rd
+++ b/man/def_net_module2.Rd
@@ -5,7 +5,8 @@
 \title{Identify the the edge of the modules (blocks) within the net connectivity matrix}
 \usage{
 def_net_module2(core_sub_jaccard_dist, sub_jaccard_dist,
-  min.connectivity = 0.2, min.size = 5, start_idx = 1, allow.gap = 1)
+  min.connectivity = 0.2, min.size = 5, start_idx = 1,
+  allow.gap = 1)
 }
 \arguments{
 \item{core_sub_jaccard_dist}{preprocessed sub_jaccard_dist matrix (after applying filter, binarized the data)}
@@ -31,4 +32,3 @@ def_net_modules2(core_sub_jaccard_dist, sub_jaccard_dist, min.connectivity=0.2,
 \keyword{co-expression,}
 \keyword{connectivity}
 \keyword{network,}
-
diff --git a/man/def_net_modules.Rd b/man/def_net_modules.Rd
index b53a0ca..458eb0d 100644
--- a/man/def_net_modules.Rd
+++ b/man/def_net_modules.Rd
@@ -29,4 +29,3 @@ def_net_modules(data, tao=0.5, beta=10, num_feature=0.01)
 \keyword{co-expression,}
 \keyword{connectivity}
 \keyword{network,}
-
diff --git a/man/deseq_norm.Rd b/man/deseq_norm.Rd
index 1e04c3f..1d8d6d7 100644
--- a/man/deseq_norm.Rd
+++ b/man/deseq_norm.Rd
@@ -16,4 +16,3 @@ Normalize data through DESeq size factor
 deseq_norm(countdata)
 }
 \keyword{deseq}
-
diff --git a/man/detect_genecnt_ID.Rd b/man/detect_genecnt_ID.Rd
deleted file mode 100644
index d702660..0000000
--- a/man/detect_genecnt_ID.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/format_utils.R
-\name{detect_genecnt_id}
-\alias{detect_genecnt_id}
-\title{Automatically convert genecnt into Entrez ID}
-\usage{
-detect_genecnt_id(data, sum.method = "mean")
-}
-\arguments{
-\item{data}{Gene id list you want to convert}
-}
-\description{
-Standize gene id into Entrez ID
-}
-\examples{
-detect_genecnt_id("TP53")
-}
-\keyword{conversion}
-
diff --git a/man/detect_genecnt_platform.Rd b/man/detect_genecnt_platform.Rd
index 0417508..241a9d4 100644
--- a/man/detect_genecnt_platform.Rd
+++ b/man/detect_genecnt_platform.Rd
@@ -17,4 +17,3 @@ leave normal gene_symbols intact
 detect_genecnt_platform("TP53")
 }
 \keyword{standardize}
-
diff --git a/man/ext_gene_function.Rd b/man/ext_gene_function.Rd
index d2b6068..08e26a5 100644
--- a/man/ext_gene_function.Rd
+++ b/man/ext_gene_function.Rd
@@ -20,4 +20,3 @@ ext_gene_function()
 }
 \keyword{annotate}
 \keyword{ensembl,}
-
diff --git a/man/extract_data_by_mad.Rd b/man/extract_data_by_mad.Rd
index cad34db..26d5f36 100644
--- a/man/extract_data_by_mad.Rd
+++ b/man/extract_data_by_mad.Rd
@@ -19,4 +19,3 @@ extract_data_by_mad(mtcars, topN=10, type="data")
 }
 \keyword{MAD,}
 \keyword{extract}
-
diff --git a/man/extract_data_by_math.Rd b/man/extract_data_by_math.Rd
index b533e72..b05072a 100644
--- a/man/extract_data_by_math.Rd
+++ b/man/extract_data_by_math.Rd
@@ -20,4 +20,3 @@ extract_data_by_math(mtcars, topN=10, type="data", math="mean")
 }
 \keyword{data}
 \keyword{extraction}
-
diff --git a/man/gene_convert_human_to_mouse.Rd b/man/gene_convert_human_to_mouse.Rd
index 6cba514..44e8bd5 100644
--- a/man/gene_convert_human_to_mouse.Rd
+++ b/man/gene_convert_human_to_mouse.Rd
@@ -17,4 +17,3 @@ we will simply convert the first letter into Capital and return it
 gene_convert_human_to_mouse("TP53")
 }
 \keyword{standardize}
-
diff --git a/man/gene_convert_mouse_to_human.Rd b/man/gene_convert_mouse_to_human.Rd
index bdb2c7f..a9d8354 100644
--- a/man/gene_convert_mouse_to_human.Rd
+++ b/man/gene_convert_mouse_to_human.Rd
@@ -16,4 +16,3 @@ This function allows you to express your love of cats.
 gene_convert_human_to_mouse("Trp53")
 }
 \keyword{standardize}
-
diff --git a/man/get_ClaNC_group.Rd b/man/get_ClaNC_group.Rd
index 9497533..326aab9 100644
--- a/man/get_ClaNC_group.Rd
+++ b/man/get_ClaNC_group.Rd
@@ -16,4 +16,3 @@ Extract which group each point belongs to
 get_ClaNC_group()
 }
 \keyword{ClaNC}
-
diff --git a/man/getcentroid.Rd b/man/getcentroid.Rd
new file mode 100644
index 0000000..2b49a46
--- /dev/null
+++ b/man/getcentroid.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/nmf_utils.R
+\name{getcentroid}
+\alias{getcentroid}
+\title{Get centroid from data frame}
+\usage{
+getcentroid(df, method = "mean")
+}
+\arguments{
+\item{df}{gene count table}
+
+\item{method}{mean or median for calculating centroid}
+}
+\description{
+Get centroid from data frame
+}
+\keyword{NMF}
+\keyword{centroid}
+\keyword{iterative}
diff --git a/man/heatmap.3.Rd b/man/heatmap.3.Rd
index 3501041..69735c4 100644
--- a/man/heatmap.3.Rd
+++ b/man/heatmap.3.Rd
@@ -14,13 +14,13 @@ heatmap.3(x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE,
   na.color = par("bg"), trace = c("none", "column", "row", "both"),
   tracecol = "cyan", hline = median(breaks), vline = median(breaks),
   linecol = tracecol, margins = c(5, 5), ColSideColors, RowSideColors,
-  side.height.fraction = 0.3, cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 +
-  1/log10(nc), labRow = NULL, labCol = NULL, key = TRUE, keysize = 1.5,
-  density.info = c("none", "histogram", "density"), denscol = tracecol,
-  symkey = max(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25,
-  main = NULL, xlab = NULL, ylab = NULL, lmat = NULL, lhei = NULL,
-  lwid = NULL, ColSideColorsSize = 1, RowSideColorsSize = 1,
-  KeyValueName = "Value", ...)
+  side.height.fraction = 0.3, cexRow = 0.2 + 1/log10(nr),
+  cexCol = 0.2 + 1/log10(nc), labRow = NULL, labCol = NULL,
+  key = TRUE, keysize = 1.5, density.info = c("none", "histogram",
+  "density"), denscol = tracecol, symkey = max(x < 0, na.rm = TRUE) ||
+  symbreaks, densadj = 0.25, main = NULL, xlab = NULL, ylab = NULL,
+  lmat = NULL, lhei = NULL, lwid = NULL, ColSideColorsSize = 1,
+  RowSideColorsSize = 1, KeyValueName = "Value", ...)
 }
 \arguments{
 \item{x}{data}
@@ -32,4 +32,3 @@ Published version of heatmap.3, with more options
 heatmap.3(iris)
 }
 \keyword{heatmap}
-
diff --git a/man/is.whole.Rd b/man/is.whole.Rd
index 10448ed..c6f2ae3 100644
--- a/man/is.whole.Rd
+++ b/man/is.whole.Rd
@@ -9,4 +9,3 @@ is.whole(a, tol = 1e-07)
 \description{
 Check whether it is a integer whole value
 }
-
diff --git a/man/iter_nmf.Rd b/man/iter_nmf.Rd
index 43952f7..6206bfc 100644
--- a/man/iter_nmf.Rd
+++ b/man/iter_nmf.Rd
@@ -4,8 +4,9 @@
 \alias{iter_nmf}
 \title{Run iterative NMF for K=2 until it cannot no longer separate samples}
 \usage{
-iter_nmf(rawdata, nrun = 10, round = 1, min.sample = 10, mad = 5000,
-  silhouette = 0.95, w.silhouette = 0.7, w.min.sample = 10, ncores = 8)
+iter_nmf(rawdata, nrun = 10, round = 1, min.sample = 10,
+  mad = 5000, silhouette = 0.95, w.silhouette = 0.7,
+  w.min.sample = 10, ncores = 8)
 }
 \arguments{
 \item{rawdata}{gene count table}
@@ -26,4 +27,3 @@ iter_nmf(rawdata, nrun=10, mad=5000)
 }
 \keyword{NMF}
 \keyword{iterative}
-
diff --git a/man/load_genelist.Rd b/man/load_genelist.Rd
index 2a67c72..f22ad0f 100644
--- a/man/load_genelist.Rd
+++ b/man/load_genelist.Rd
@@ -18,4 +18,3 @@ Load predefined gene list files for heatmap (clustering) result
 load_genelist("data", ".txt")
 }
 \keyword{lodad}
-
diff --git a/man/load_geneset.Rd b/man/load_geneset.Rd
index 101c18a..1da5868 100644
--- a/man/load_geneset.Rd
+++ b/man/load_geneset.Rd
@@ -18,4 +18,3 @@ Load predefined gene list files for gene set enrichment analysis (GSEA)
 load_geneset("data", ".txt")
 }
 \keyword{lodad}
-
diff --git a/man/module_finder.Rd b/man/module_finder.Rd
index 9ac5ddc..628c099 100644
--- a/man/module_finder.Rd
+++ b/man/module_finder.Rd
@@ -19,4 +19,3 @@ module_finder(mtcars)
 \keyword{co-expression}
 \keyword{module,}
 \keyword{network,}
-
diff --git a/man/multiplot.Rd b/man/multiplot.Rd
index 79539b9..bf05f2c 100644
--- a/man/multiplot.Rd
+++ b/man/multiplot.Rd
@@ -21,4 +21,3 @@ then plot 1 will go in the upper left, 2 will go in the upper right, and
 multiplot()
 }
 \keyword{multiplot}
-
diff --git a/man/mutual_info_from_confmatrix.Rd b/man/mutual_info_from_confmatrix.Rd
index 31aa1ff..b3132b1 100644
--- a/man/mutual_info_from_confmatrix.Rd
+++ b/man/mutual_info_from_confmatrix.Rd
@@ -20,4 +20,3 @@ Calculate Mutual information from confusion matrix
 }
 \keyword{information}
 \keyword{mutual}
-
diff --git a/man/mutual_info_from_vector.Rd b/man/mutual_info_from_vector.Rd
index 52c6cde..586148c 100644
--- a/man/mutual_info_from_vector.Rd
+++ b/man/mutual_info_from_vector.Rd
@@ -9,4 +9,3 @@ mutual_info_from_vector(x, y, base = exp(1))
 \description{
 first generate summary table, then use equation to calculate mutual info
 }
-
diff --git a/man/my.write.matrix.Rd b/man/my.write.matrix.Rd
index d5b4696..e214a6c 100644
--- a/man/my.write.matrix.Rd
+++ b/man/my.write.matrix.Rd
@@ -4,9 +4,9 @@
 \alias{my.write.matrix}
 \title{Own version of writing matrix output}
 \usage{
-my.write.matrix(x, file = "", sep = "\\t", col.names = T, append = F,
-  row.names = F, justify = c("none", "left", "right"), pval = NULL,
-  newline = "\\n", names = NULL)
+my.write.matrix(x, file = "", sep = "\\t", col.names = T,
+  append = F, row.names = F, justify = c("none", "left", "right"),
+  pval = NULL, newline = "\\n", names = NULL)
 }
 \arguments{
 \item{countdata}{integer data frame}
@@ -18,4 +18,3 @@ Own version of writing matrix output
 my.write.matrix(data)
 }
 \keyword{write.matrix}
-
diff --git a/man/myHeatmap.3.Rd b/man/myHeatmap.3.Rd
index 92888b1..121f25c 100644
--- a/man/myHeatmap.3.Rd
+++ b/man/myHeatmap.3.Rd
@@ -7,15 +7,15 @@
 myHeatmap.3(data, color = rev(brewer.pal(8, "RdYlBu")), type = "cor",
   save.image = F, width = 18, height = 18, title = "",
   file.prefix = "heatmap", ColSideColors = NULL,
-  ColSideColors.name = NULL, ColSideColorsSize = 1, RowSideColors = NULL,
-  RowSideColors.name = NULL, RowSideColorsSize = 1,
-  reorderfun = function(d, w) reorder(d, w), Colv = NULL, Rowv = NULL,
-  na.rm = T, cor.method = "pearson", dist.m = "euclidean",
-  hclust.m = "ward.D2", scale = "row", scale.method = "mean",
-  scale.first = F, dendrogram = "both", dendro.ord = "auto",
-  notecex = 1.4, notecol = "black", col.legend = F, row.legend = F,
-  labRow = T, labCol = T, cexRow = 1.1, cexCol = 1.1, lhei = c(1.3,
-  7), lwid = c(1, 7))
+  ColSideColors.name = NULL, ColSideColorsSize = 1,
+  RowSideColors = NULL, RowSideColors.name = NULL,
+  RowSideColorsSize = 1, reorderfun = function(d, w) reorder(d, w),
+  Colv = NULL, Rowv = NULL, na.rm = T, cor.method = "pearson",
+  dist.m = "euclidean", hclust.m = "ward.D2", scale = "row",
+  scale.method = "mean", scale.first = F, dendrogram = "both",
+  dendro.ord = "auto", notecex = 1.4, notecol = "black",
+  col.legend = F, row.legend = F, labRow = T, labCol = T,
+  cexRow = 1.1, cexCol = 1.1, lhei = c(1.3, 7), lwid = c(1, 7))
 }
 \arguments{
 \item{love}{Do you love cats? Defaults to TRUE.}
@@ -24,4 +24,3 @@ myHeatmap.3(data, color = rev(brewer.pal(8, "RdYlBu")), type = "cor",
 This function allows you to express your love of cats.
 }
 \keyword{cats}
-
diff --git a/man/myNMF.Rd b/man/myNMF.Rd
index 5b55ba8..55b5a2d 100644
--- a/man/myNMF.Rd
+++ b/man/myNMF.Rd
@@ -40,4 +40,3 @@ myNMF(data, mode="estim", cluster=3, nrun=20)
 }
 \keyword{NMF}
 \keyword{cluster}
-
diff --git a/man/myboxplot.Rd b/man/myboxplot.Rd
index 0ae4403..f1d4ee3 100644
--- a/man/myboxplot.Rd
+++ b/man/myboxplot.Rd
@@ -6,7 +6,8 @@
 \usage{
 myboxplot(data, prefix = "Boxplot", method = "vioplot", title = "",
   ylim = c(0.6, 0.85), save.plot = F, axis.text.size = 14,
-  axis.title.size = 16, legend.position = "right", vio.add.method = "dot")
+  axis.title.size = 16, legend.position = "right",
+  vio.add.method = "dot")
 }
 \arguments{
 \item{love}{Do you love cats? Defaults to TRUE.}
@@ -18,4 +19,3 @@ This function allows you to express your love of cats.
 myboxplot()
 }
 \keyword{cats}
-
diff --git a/man/myd3Heatmap.Rd b/man/myd3Heatmap.Rd
index 67ed89d..2db321e 100644
--- a/man/myd3Heatmap.Rd
+++ b/man/myd3Heatmap.Rd
@@ -6,15 +6,17 @@
 \usage{
 myd3Heatmap(data, color = rev(brewer.pal(8, "RdYlBu")), type = "cor",
   width = 18, height = 18, title = "", file.prefix = "heatmap",
-  ColSideColors = NULL, ColSideColors.name = NULL, ColSideColorsSize = 1,
-  RowSideColors = NULL, RowSideColors.name = NULL, RowSideColorsSize = 1,
-  dendrogram = "both", dendro.ord = "auto", reorderfun = function(d, w)
-  reorder(d, w), Colv = NULL, Rowv = NULL, na.rm = T,
+  ColSideColors = NULL, ColSideColors.name = NULL,
+  ColSideColorsSize = 1, RowSideColors = NULL,
+  RowSideColors.name = NULL, RowSideColorsSize = 1,
+  dendrogram = "both", dendro.ord = "auto", reorderfun = function(d,
+  w) reorder(d, w), Colv = NULL, Rowv = NULL, na.rm = T,
   cor.method = "pearson", dist.m = "euclidean", hclust.m = "ward.D2",
-  scale = "row", scale.method = "mean", scale.first = F, notecex = 1.4,
-  notecol = "black", show_grid = FALSE, anim_duration = 0.1,
-  col.legend = F, row.legend = F, labRow = T, labCol = T, cexRow = 1,
-  cexCol = 1, lhei = c(1.5, 7), lwid = c(1, 7))
+  scale = "row", scale.method = "mean", scale.first = F,
+  notecex = 1.4, notecol = "black", show_grid = FALSE,
+  anim_duration = 0.1, col.legend = F, row.legend = F, labRow = T,
+  labCol = T, cexRow = 1, cexCol = 1, lhei = c(1.5, 7),
+  lwid = c(1, 7))
 }
 \arguments{
 \item{data}{data.frame for plot}
@@ -27,4 +29,3 @@ myd3Heatmap(mtcars)
 }
 \keyword{d3heatmap}
 \keyword{heatmap,}
-
diff --git a/man/myfread.table.Rd b/man/myfread.table.Rd
index 8819d13..e238c84 100644
--- a/man/myfread.table.Rd
+++ b/man/myfread.table.Rd
@@ -18,4 +18,3 @@ myfread.table(system.file('sake', package='sake'))
 }
 \keyword{data}
 \keyword{read}
-
diff --git a/man/name_to_color.Rd b/man/name_to_color.Rd
index 6b80d91..81707f1 100644
--- a/man/name_to_color.Rd
+++ b/man/name_to_color.Rd
@@ -18,4 +18,3 @@ This function convert the sample_name in the data into different colors
 name_to_color(c("group1", "group1", "group2", "group2"))
 }
 \keyword{color}
-
diff --git a/man/nmf_estim_plot.Rd b/man/nmf_estim_plot.Rd
index b5a3473..b92650c 100644
--- a/man/nmf_estim_plot.Rd
+++ b/man/nmf_estim_plot.Rd
@@ -16,4 +16,3 @@ This function allows you to express your love of cats.
 nmf_estim_plot(estim.r)
 }
 \keyword{silhouette}
-
diff --git a/man/nmf_extract_feature.Rd b/man/nmf_extract_feature.Rd
index c521126..3ca17c4 100644
--- a/man/nmf_extract_feature.Rd
+++ b/man/nmf_extract_feature.Rd
@@ -28,4 +28,3 @@ nmf_extract_feature(nmf_res)
 }
 \keyword{NMF}
 \keyword{feature}
-
diff --git a/man/nmf_extract_group.Rd b/man/nmf_extract_group.Rd
index 9a60cb4..ae3b7b5 100644
--- a/man/nmf_extract_group.Rd
+++ b/man/nmf_extract_group.Rd
@@ -19,4 +19,3 @@ nmf_extract_group(nmf_res)
 }
 \keyword{NMF}
 \keyword{groups}
-
diff --git a/man/nmf_plot.Rd b/man/nmf_plot.Rd
index 7decdff..ec6f4ba 100644
--- a/man/nmf_plot.Rd
+++ b/man/nmf_plot.Rd
@@ -22,4 +22,3 @@ nmf_plot(nmf_res)
 }
 \keyword{NMF}
 \keyword{feature}
-
diff --git a/man/nmf_select_best_k.Rd b/man/nmf_select_best_k.Rd
index 841692f..83951b1 100644
--- a/man/nmf_select_best_k.Rd
+++ b/man/nmf_select_best_k.Rd
@@ -20,4 +20,3 @@ nmf_select_best_k(nmf_res)
 }
 \keyword{NMF}
 \keyword{feature}
-
diff --git a/man/nmf_silhouette_plot.Rd b/man/nmf_silhouette_plot.Rd
index ed1e6d3..1da7ba8 100644
--- a/man/nmf_silhouette_plot.Rd
+++ b/man/nmf_silhouette_plot.Rd
@@ -16,4 +16,3 @@ This function allows you to express your love of cats.
 nmf_silhouette_plot(res)
 }
 \keyword{silhouette}
-
diff --git a/man/nmf_summary.Rd b/man/nmf_summary.Rd
index bfe765a..e3f5eb8 100644
--- a/man/nmf_summary.Rd
+++ b/man/nmf_summary.Rd
@@ -20,4 +20,3 @@ nmf_summary(data)
 }
 \keyword{NMF}
 \keyword{feature}
-
diff --git a/man/norm_factors.Rd b/man/norm_factors.Rd
index d3e6b5d..059a86d 100644
--- a/man/norm_factors.Rd
+++ b/man/norm_factors.Rd
@@ -17,4 +17,3 @@ norm_factors(mtcars)
 }
 \keyword{deseq,}
 \keyword{normalization}
-
diff --git a/man/parse_tsne_res.Rd b/man/parse_tsne_res.Rd
index d673183..2d8f750 100644
--- a/man/parse_tsne_res.Rd
+++ b/man/parse_tsne_res.Rd
@@ -17,4 +17,3 @@ tsne_out <- run_tsne(mtcar, perplexity=3)
 parse_tsne_res(tsne_out)
 }
 \keyword{cats}
-
diff --git a/man/pcaplot.Rd b/man/pcaplot.Rd
index cbcb89e..1bd639d 100644
--- a/man/pcaplot.Rd
+++ b/man/pcaplot.Rd
@@ -4,11 +4,10 @@
 \alias{pcaplot}
 \title{simple PCA plot}
 \usage{
-pcaplot(data, takelog = FALSE, center = TRUE, scale = FALSE, pca_x = 1,
-  pca_y = 2, group = NULL, opacity = 0.6, plotsize = 7, labsize = 4,
-  legend = TRUE)
+pcaplot(data, takelog = FALSE, center = TRUE, scale = FALSE,
+  pca_x = 1, pca_y = 2, group = NULL, opacity = 0.6,
+  plotsize = 7, labsize = 4, legend = TRUE)
 }
 \description{
 This is a simple version of PCA plot
 }
-
diff --git a/man/plot_gene_expression.Rd b/man/plot_gene_expression.Rd
index b61d96e..b2a38ca 100644
--- a/man/plot_gene_expression.Rd
+++ b/man/plot_gene_expression.Rd
@@ -4,8 +4,9 @@
 \alias{plot_gene_expression}
 \title{Plot expression for each gene}
 \usage{
-plot_gene_expression(data, gene, groups, type = "boxplot", data.return = f,
-  ylim = c(0, 20), title = null, las = 1, cex.axis = 1)
+plot_gene_expression(data, gene, groups, type = "boxplot",
+  data.return = f, ylim = c(0, 20), title = null, las = 1,
+  cex.axis = 1)
 }
 \arguments{
 \item{love}{Do you love cats? Defaults to TRUE.}
@@ -17,4 +18,3 @@ This function allows you to express your love of cats.
 cat_function()
 }
 \keyword{cats}
-
diff --git a/man/plot_modules.Rd b/man/plot_modules.Rd
index f1c8e56..8d6bf5f 100644
--- a/man/plot_modules.Rd
+++ b/man/plot_modules.Rd
@@ -22,4 +22,3 @@ plot_modules(core_sub_jaccard_dist, final_genelist)
 \keyword{co-expression,}
 \keyword{connectivity}
 \keyword{network,}
-
diff --git a/man/plot_tsne.Rd b/man/plot_tsne.Rd
index 4a5baca..4614253 100644
--- a/man/plot_tsne.Rd
+++ b/man/plot_tsne.Rd
@@ -5,9 +5,10 @@
 \title{Plot t-SNE results}
 \usage{
 plot_tsne(tsne_out, color = NULL, alpha = 1, title = "tSNE",
-  brewer = "naikai", add.centroids = F, add.line = F, add.errorbar = F,
-  add.label = F, label.size = 3, conf = F, add.legend = F,
-  save.plot = T, real.plot = T, point.size = 3, centroid.size = 6)
+  brewer = "naikai", add.centroids = F, add.line = F,
+  add.errorbar = F, add.label = F, label.size = 3, conf = F,
+  add.legend = F, save.plot = T, real.plot = T, point.size = 3,
+  centroid.size = 6)
 }
 \arguments{
 \item{tsne_out}{t-SNE results from run_tSNE}
@@ -29,4 +30,3 @@ tsne_out <- parse_tsne_res(tsne_out)
 plot_tsne(tsne_out)
 }
 \keyword{tsne}
-
diff --git a/man/predict_from_centroid.Rd b/man/predict_from_centroid.Rd
index 07c98af..9abeacd 100644
--- a/man/predict_from_centroid.Rd
+++ b/man/predict_from_centroid.Rd
@@ -4,7 +4,8 @@
 \alias{predict_from_centroid}
 \title{Predict group assignment from centroids}
 \usage{
-predict_from_centroid(centroids, data, scale = "none", method = "spearman")
+predict_from_centroid(centroids, data, scale = "none",
+  method = "spearman")
 }
 \arguments{
 \item{centroids}{centroids for each group}
@@ -18,4 +19,3 @@ Predict group assignment from centroids
 predict_from_centroid()
 }
 \keyword{centroid}
-
diff --git a/man/preprocessNetCon.Rd b/man/preprocessNetCon.Rd
index ee9eb78..cc3535a 100644
--- a/man/preprocessNetCon.Rd
+++ b/man/preprocessNetCon.Rd
@@ -4,8 +4,8 @@
 \alias{preprocessNetCon}
 \title{Preprocess the connecitivty matrix based on mean connectivity and binary switch}
 \usage{
-preprocessNetCon(sub_jaccard_dist, rmv.filter = 0.5, binary.filter = 0.75,
-  plot = F)
+preprocessNetCon(sub_jaccard_dist, rmv.filter = 0.5,
+  binary.filter = 0.75, plot = F)
 }
 \arguments{
 \item{data}{Input expression data}
@@ -28,4 +28,3 @@ preprocessNetCon(sub_jaccard_dist, rmv.filter=0.5, binary.filter=0.75, plot=F)
 \keyword{co-expression,}
 \keyword{connectivity}
 \keyword{network,}
-
diff --git a/man/reorderfun.Rd b/man/reorderfun.Rd
index a3bfc5b..bbfbe1d 100644
--- a/man/reorderfun.Rd
+++ b/man/reorderfun.Rd
@@ -18,4 +18,3 @@ Reorder dendrogram based on mean expression for RNA-Seq
 reorderfun()
 }
 \keyword{reorder}
-
diff --git a/man/rmv_constant_0.Rd b/man/rmv_constant_0.Rd
index 27e0577..32f44b0 100644
--- a/man/rmv_constant_0.Rd
+++ b/man/rmv_constant_0.Rd
@@ -20,4 +20,3 @@ You can specify the percentage of 0s as the threshold
 rmv_constant_0(data, by="row", pct=0.75)
 }
 \keyword{rmv_constant_var}
-
diff --git a/man/run_CV.Rd b/man/run_CV.Rd
index 40f7733..500612e 100644
--- a/man/run_CV.Rd
+++ b/man/run_CV.Rd
@@ -16,4 +16,3 @@ Run Cross-Validation
 run_CV(cv_data)
 }
 \keyword{cross-validation}
-
diff --git a/man/run_ClaNC.Rd b/man/run_ClaNC.Rd
index c932981..d09ed1f 100644
--- a/man/run_ClaNC.Rd
+++ b/man/run_ClaNC.Rd
@@ -4,8 +4,9 @@
 \alias{run_ClaNC}
 \title{ClaNC run}
 \usage{
-run_ClaNC(data, groups, ColSideColors, active.features = 20, est.num = 20,
-  select.features = 10, file.prefix = "ClaNC", skip.est = F)
+run_ClaNC(data, groups, ColSideColors, active.features = 20,
+  est.num = 20, select.features = 10, file.prefix = "ClaNC",
+  skip.est = F)
 }
 \arguments{
 \item{love}{Do you love cats? Defaults to TRUE.}
@@ -17,4 +18,3 @@ This function allows you to express your love of cats.
 cat_function()
 }
 \keyword{cats}
-
diff --git a/man/run_CoExpression.Rd b/man/run_CoExpression.Rd
index 1757053..ae0ce4d 100644
--- a/man/run_CoExpression.Rd
+++ b/man/run_CoExpression.Rd
@@ -7,8 +7,8 @@
 2. Convert the matrix into binary based on quantile connectivity'}
 \usage{
 run_CoExpression(expdata, thresh = "soft", tao = 0.7, beta = 10,
-  method = "Pearson", folderName0 = "Module", avg_con_thresh = 0.00015,
-  save.data = F)
+  method = "Pearson", folderName0 = "Module",
+  avg_con_thresh = 0.00015, save.data = F)
 }
 \arguments{
 \item{tao}{threshold for hard transformation}
@@ -30,4 +30,3 @@ run_CoExpression(expdata)
 \keyword{co-expression,}
 \keyword{connectivity}
 \keyword{network,}
-
diff --git a/man/run_DESeq2.Rd b/man/run_DESeq2.Rd
index a8d3fc4..4575b92 100644
--- a/man/run_DESeq2.Rd
+++ b/man/run_DESeq2.Rd
@@ -13,4 +13,3 @@ This function allows you to run DESeq2 if provided required data
 run_DESeq2()
 }
 \keyword{DESeq2}
-
diff --git a/man/run_icash.Rd b/man/run_icash.Rd
index 377fc9c..aef2152 100644
--- a/man/run_icash.Rd
+++ b/man/run_icash.Rd
@@ -9,4 +9,3 @@ run_icash()
 \description{
 Wrapper function to run the icahs Shiny App
 }
-
diff --git a/man/run_tsne.Rd b/man/run_tsne.Rd
index dbcd607..94a7b24 100644
--- a/man/run_tsne.Rd
+++ b/man/run_tsne.Rd
@@ -25,4 +25,3 @@ This function allows you to run t-SNE using multi-cores
 run_tsne(mtcars, iter=200, perplexity = 2, cores=4)
 }
 \keyword{t-SNE}
-
diff --git a/man/sake.Rd b/man/sake.Rd
index a851b49..f8fe3b9 100644
--- a/man/sake.Rd
+++ b/man/sake.Rd
@@ -9,4 +9,3 @@
 This tool can help you quickly navigate through the expression profile,
 Using NMF method for unsupervised clustering.
 }
-
diff --git a/man/scale_data.Rd b/man/scale_data.Rd
index 7570817..d75ee29 100644
--- a/man/scale_data.Rd
+++ b/man/scale_data.Rd
@@ -22,4 +22,3 @@ This function allows you to scale the data based on your metrics of interest
 scale_data(mtcars)
 }
 \keyword{scale}
-
diff --git a/man/screenshot_plotly.Rd b/man/screenshot_plotly.Rd
index 8a17d46..33a1aaf 100644
--- a/man/screenshot_plotly.Rd
+++ b/man/screenshot_plotly.Rd
@@ -14,4 +14,3 @@ screenshot_plotly(x, file = "webshot.png", ...)
 \description{
 Screen shot of plotly object
 }
-
diff --git a/man/select_n_pct.Rd b/man/select_n_pct.Rd
index 7d4df2f..de976d7 100644
--- a/man/select_n_pct.Rd
+++ b/man/select_n_pct.Rd
@@ -20,4 +20,3 @@ select_n_pct(c(1,23,1,412,51,231,516,1,23,13,3,5,1), 10)
 \keyword{n}
 \keyword{percent}
 \keyword{top}
-
diff --git a/man/select_top_n.Rd b/man/select_top_n.Rd
index 27b41e2..a124464 100644
--- a/man/select_top_n.Rd
+++ b/man/select_top_n.Rd
@@ -20,4 +20,3 @@ Select top # from a vector
 select_top_n(mtcars, 100, bottom=F)
 }
 \keyword{select}
-
diff --git a/man/simpleCap.Rd b/man/simpleCap.Rd
index ce3364e..a1580b2 100644
--- a/man/simpleCap.Rd
+++ b/man/simpleCap.Rd
@@ -16,4 +16,3 @@ Convert letter to capitalization
 simpleCap("meat is good")
 }
 \keyword{standardize}
-
diff --git a/man/summarize_module2.Rd b/man/summarize_module2.Rd
index b589bfb..14db213 100644
--- a/man/summarize_module2.Rd
+++ b/man/summarize_module2.Rd
@@ -5,7 +5,8 @@
 \title{Identify the the edge of the modules (blocks) within the net connectivity matrix}
 \usage{
 summarize_module2(core_sub_jaccard_dist, old, current, blk_cnt, genenames,
-  original_names, res_summary, res_genelist, size, min.size = 5, start_idx)
+  original_names, res_summary, res_genelist, size, min.size = 5,
+  start_idx)
 }
 \arguments{
 \item{core_sub_jaccard_dist}{jaccard distance for sub core genes}
@@ -20,4 +21,3 @@ summarize_module(core_sub_jaccard_dist, sub_jaccard_dist, min.connectivity=0.2,
 }
 \keyword{co-expression}
 \keyword{network,}
-
diff --git a/man/top_genes.Rd b/man/top_genes.Rd
index fddead3..e47a557 100644
--- a/man/top_genes.Rd
+++ b/man/top_genes.Rd
@@ -22,4 +22,3 @@ top_genes(data)
 \keyword{n}
 \keyword{percent}
 \keyword{top}
-
diff --git a/man/vst.Rd b/man/vst.Rd
index 6960e9a..5a19588 100644
--- a/man/vst.Rd
+++ b/man/vst.Rd
@@ -17,4 +17,3 @@ vst(countdata)
 }
 \keyword{deseq2}
 \keyword{vst,}
-
diff --git a/man/weighted.silhouette.Rd b/man/weighted.silhouette.Rd
index 4896e49..1931d3b 100644
--- a/man/weighted.silhouette.Rd
+++ b/man/weighted.silhouette.Rd
@@ -12,4 +12,3 @@ weighted.silhouette(nmf_groups)
 \description{
 calculate weighted silhouette_width as threshold for running iter_NMF
 }
-
diff --git a/man/wgcna_ext_hubgenes.Rd b/man/wgcna_ext_hubgenes.Rd
index 0c14520..690478d 100644
--- a/man/wgcna_ext_hubgenes.Rd
+++ b/man/wgcna_ext_hubgenes.Rd
@@ -26,4 +26,3 @@ wgcna_ext_hubgenes(datExpr)
 \keyword{co-expression,}
 \keyword{network}
 \keyword{wgcna,}
-