diff --git a/DESCRIPTION b/DESCRIPTION
index 390729f..266cc05 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -24,4 +24,4 @@ Imports:
     dplyr,
     cowplot,
     reshape2
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.3
diff --git a/NAMESPACE b/NAMESPACE
index 1b44fd1..ad3349d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export()
 export(GEP_makeMean)
 export(addRandToSampTab)
 export(addToST)
@@ -26,12 +25,12 @@ export(findAvgLabel)
 export(findBestPairs)
 export(findClassyGenes)
 export(findVarGenes)
-export(get_cate)
 export(getGenesFromGO)
 export(getSpecGenes)
 export(getTopGenes)
 export(getTopGenesList)
 export(getUniqueGenes)
+export(get_cate)
 export(gnrAll)
 export(gnrBP)
 export(harmonize)
@@ -109,7 +108,5 @@ export(utils_strip_fname)
 export(utils_stripwhite)
 export(weighted_down)
 import(parallel)
-import(umap)
-import(viridis)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(randomForest,randomForest)
diff --git a/R/utils.R b/R/utils.R
index e15a77f..1143989 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -25,7 +25,7 @@ ctRename<-function(sampTab, annCol, oldName, newName){
   xnot<-which(colnames(sampTab)!=annCol)
   ans<-sampTab[,xnot]
   cbind(ans, newAnn=newann)
-} 
+}
 
 #' @title
 #' Split Sample Table
@@ -41,13 +41,13 @@ ctRename<-function(sampTab, annCol, oldName, newName){
 #'
 #' @export
 splitCommon<-function(sampTab, ncells = 50, dLevel="cell_ontology_class", cells_reserved = 3){
-  
+
   cts<-unique(as.vector(sampTab[,dLevel]))
 
   if(sum(is.na(cts)) > 0){
     stop("There are NAs in your training labels, please remove them first!")
   }
-  
+
   trainingids<-vector()
   for(ct in cts){
     cat(ct,": ")
@@ -102,7 +102,7 @@ loadLoomExpCluster<-function# load a loom object containing expression  + cluste
   expMat<- t(lfile[["matrix"]][1:length(cellNames),])
   rownames(expMat)<-geneNames
   colnames(expMat)<-cellNames
-  
+
   cluster_old <- lfile[['col_attrs']][[xname]][]
 
   sampTab <- data.frame(cell_name=cellNames, cluster=cluster_old)
@@ -117,7 +117,7 @@ loadLoomExpCluster<-function# load a loom object containing expression  + cluste
 #' @export
 getGenesFromGO<-function# return the entrez gene ids of a given a GOID, for now assumes mouse
 (GOID, # GO id to find genes for
- annList 
+ annList
 ){
   sort(as.vector(unlist(annList[['egSymbols']][annList[['goegs']][[GOID]]])));
 }
@@ -149,15 +149,15 @@ GEP_makeMean<-function
  groupings,
  type='mean'
 ){
-  
-  
+
+
   ans<-data.frame();
   grps<-unique(groupings);
   if(type=='mean'){
     for(grp in grps){
       gi<-which(groupings==grp);
       if(length(gi)==1){
-        
+
         if(nrow(ans)==0){
           ans<-data.frame(exp[,gi]);
         }else{
@@ -187,7 +187,7 @@ GEP_makeMean<-function
       }
     }
   }
-  
+
   colnames(ans)<-grps;
   ans;
   ### data.frame of mean or median-ed data based on given groupings
@@ -215,8 +215,8 @@ library(GO.db)
 #'
 #' 1-PCC distance
 #' @param x numeric matrix
-#' 
-#' @return distance matrix  
+#'
+#' @return distance matrix
 #'
 #' @examples
 #' xdist<-utils_myDist(t(expDat))
@@ -254,7 +254,7 @@ utils_loadObject<-function
 #'
 #' @export
 utils_stripwhite<-function
-### 
+###
 (string
  #### string
  ){
@@ -268,7 +268,7 @@ utils_stripwhite<-function
 #'
 #' @export
 utils_myDate<-function
-### 
+###
 ()
 {
   format(Sys.time(), "%b_%d_%Y");
@@ -299,11 +299,11 @@ zscore<-function
 ### compute zscore
 (x,
  ### numeric vector
- meanVal, 
- ### mean of distribution to compute zscore of x against 
+ meanVal,
+ ### mean of distribution to compute zscore of x against
  sdVal
  ### standard deviation of distribution to compute zscore of x agains
- ){ 
+ ){
   (x-meanVal)/sdVal;
   ### zscore
 }
@@ -363,7 +363,7 @@ cn_correctZmat<-function
 downSampleW<-function
 (vector,
  total=1e5,
- dThresh=0){ 
+ dThresh=0){
 
   totalSignal<-sum(vector)
   wAve<-vector/totalSignal
@@ -403,7 +403,7 @@ weighted_down<-function
     tmpAns <- expDat - t(props * rrids)
     tmpAns[which(tmpAns<dThresh)] <- 0
   }
-  
+
   tmpAns
 }
 
@@ -461,15 +461,15 @@ trans_binarize<-function
 #' @return list
 #' @export
 extractSeurat <- function(seurat_object, exp_slot_name = "counts"){
-  
+
   #extract metadata
   sampTab = seurat_object@meta.data
-  
+
   #extract expression matrix
-  expDat = as.matrix(GetAssayData(seurat_object, slot = exp_slot_name))   
-  
+  expDat = as.matrix(GetAssayData(seurat_object, slot = exp_slot_name))
+
   return(list(sampTab = sampTab, expDat = expDat))
-  
+
 }
 
 #' extract sampTab and expDat sce object into regular S3 objects
@@ -479,24 +479,24 @@ extractSeurat <- function(seurat_object, exp_slot_name = "counts"){
 #' @export
 extractSCE <- function(sce_object, exp_slot_name = "counts"){
   #extract metadata
-  sampTab = as.data.frame(colData(sce_object, internal = TRUE))
+  sampTab = as.data.frame(colData(sce_object))
   sampTab$sample_name = rownames(sampTab)
-  
+
   #extract expression matrix
-  if(exp_type == "counts"){
+  if(exp_slot_name == "counts"){
     expDat = counts(sce_object)
   }
-  
-  if(exp_type == "normcounts"){
+
+  if(exp_slot_name == "normcounts"){
     expDat = normcounts(sce_object)
   }
-  
-  if(exp_type == "logcounts"){
+
+  if(exp_slot_name == "logcounts"){
     expDat = logcounts(sce_object)
   }
-  
+
   return(list(sampTab = sampTab, expDat = expDat))
-  
+
 }
 
 #' @export
@@ -590,7 +590,7 @@ load10x<-function
 
 	# sample_name == prefix + inc
 	# sample_id == prefix + inc + barcode
-	
+
 	# barcode == barcode
 	# colnames of expDat == sample_name
 	# rownames(sampTab) = sample_name
@@ -657,7 +657,7 @@ mergeLoad10x<-function
 	##stp<-nCells
 	cat(pNames[1],"\n")
 	cat("named:",ncol(expList[[pNames[1]]][['expDat']]),"\n")
-	cat("numbered:",ncol(expList[[1]]),"\n")	
+	cat("numbered:",ncol(expList[[1]]),"\n")
 	stp<-ncol(expList[[pNames[1]]][['expDat']])
 #	for(pName in pNames){
 	for(i in seq(length(pNames))){
diff --git a/man/cn_barplot_grnSing_base.Rd b/man/cn_barplot_grnSing_base.Rd
index 5a8e86c..768325f 100644
--- a/man/cn_barplot_grnSing_base.Rd
+++ b/man/cn_barplot_grnSing_base.Rd
@@ -4,8 +4,16 @@
 \alias{cn_barplot_grnSing_base}
 \title{barplot this specific GRN}
 \usage{
-cn_barplot_grnSing_base(qScores, ctrlScores, stQuery, dLevelQ, snName,
-  ctrSamps, bOrder, sidCol = "sample_id")
+cn_barplot_grnSing_base(
+  qScores,
+  ctrlScores,
+  stQuery,
+  dLevelQ,
+  snName,
+  ctrSamps,
+  bOrder,
+  sidCol = "sample_id"
+)
 }
 \arguments{
 \item{qScores}{queryScores}
diff --git a/man/cn_clPerf.Rd b/man/cn_clPerf.Rd
index a1e094e..72b244c 100644
--- a/man/cn_clPerf.Rd
+++ b/man/cn_clPerf.Rd
@@ -4,8 +4,14 @@
 \alias{cn_clPerf}
 \title{determine performance of classification at given threshold}
 \usage{
-cn_clPerf(vect, sampTab, dLevel, classification, thresh,
-  dLevelSID = "sample_id")
+cn_clPerf(
+  vect,
+  sampTab,
+  dLevel,
+  classification,
+  thresh,
+  dLevelSID = "sample_id"
+)
 }
 \arguments{
 \item{vect}{vector of values}
diff --git a/man/cn_classAssess.Rd b/man/cn_classAssess.Rd
index 2513cb2..ee67e30 100644
--- a/man/cn_classAssess.Rd
+++ b/man/cn_classAssess.Rd
@@ -4,8 +4,13 @@
 \alias{cn_classAssess}
 \title{Assess classifiers based on validation data}
 \usage{
-cn_classAssess(ct_scores, stVal, classLevels = "description2",
-  dLevelSID = "sample_id", resolution = 0.005)
+cn_classAssess(
+  ct_scores,
+  stVal,
+  classLevels = "description2",
+  dLevelSID = "sample_id",
+  resolution = 0.005
+)
 }
 \arguments{
 \item{ct_scores}{matrix of classification scores, rows = classifiers, columns = samples, colnames=sampleids}
diff --git a/man/cn_computeAUCPR.Rd b/man/cn_computeAUCPR.Rd
index 0dcefa1..05e20ad 100644
--- a/man/cn_computeAUCPR.Rd
+++ b/man/cn_computeAUCPR.Rd
@@ -4,8 +4,12 @@
 \alias{cn_computeAUCPR}
 \title{compute AUPCR}
 \usage{
-cn_computeAUCPR(perfDF, precisionCol = "Precision",
-  recallCol = "Recall", predCol = "Predictions")
+cn_computeAUCPR(
+  perfDF,
+  precisionCol = "Precision",
+  recallCol = "Recall",
+  predCol = "Predictions"
+)
 }
 \arguments{
 \item{perfDF}{a df}
diff --git a/man/cn_eval.Rd b/man/cn_eval.Rd
index f3ebcd1..d27a64b 100644
--- a/man/cn_eval.Rd
+++ b/man/cn_eval.Rd
@@ -4,8 +4,14 @@
 \alias{cn_eval}
 \title{run cn_clPerf across thresholds}
 \usage{
-cn_eval(vect, sampTab, dLevel, classification, threshs = seq(0, 1, by =
-  0.05), dLevelSID = "sample_id")
+cn_eval(
+  vect,
+  sampTab,
+  dLevel,
+  classification,
+  threshs = seq(0, 1, by = 0.05),
+  dLevelSID = "sample_id"
+)
 }
 \arguments{
 \item{vect}{named vector}
diff --git a/man/compareGenePairs.Rd b/man/compareGenePairs.Rd
index 843bafa..f63929f 100644
--- a/man/compareGenePairs.Rd
+++ b/man/compareGenePairs.Rd
@@ -4,9 +4,16 @@
 \alias{compareGenePairs}
 \title{Compile genePairs comparison matrix}
 \usage{
-compareGenePairs(query_exp, training_exp, training_st, classCol,
-  sampleCol = NULL, RF_classifier, numPairs = 20,
-  trainingOnly = TRUE)
+compareGenePairs(
+  query_exp,
+  training_exp,
+  training_st,
+  classCol,
+  sampleCol = NULL,
+  RF_classifier,
+  numPairs = 20,
+  trainingOnly = TRUE
+)
 }
 \arguments{
 \item{query_exp}{the expression matrix of query samples}
diff --git a/man/csRenameOrth.Rd b/man/csRenameOrth.Rd
index 9f5a8b5..9074d69 100644
--- a/man/csRenameOrth.Rd
+++ b/man/csRenameOrth.Rd
@@ -4,8 +4,13 @@
 \alias{csRenameOrth}
 \title{enable cross-species comparison}
 \usage{
-csRenameOrth(expQuery, expTrain, orthTable, speciesQuery = "human",
-  speciesTrain = "mouse")
+csRenameOrth(
+  expQuery,
+  expTrain,
+  orthTable,
+  speciesQuery = "human",
+  speciesTrain = "mouse"
+)
 }
 \arguments{
 \item{expQuery}{expQuery}
diff --git a/man/findClassyGenes.Rd b/man/findClassyGenes.Rd
index f048db9..c14bb2b 100644
--- a/man/findClassyGenes.Rd
+++ b/man/findClassyGenes.Rd
@@ -4,8 +4,16 @@
 \alias{findClassyGenes}
 \title{Find Classifier-Worthy Gene Candidates}
 \usage{
-findClassyGenes(expDat, sampTab, dLevel, topX = 25, dThresh = 0,
-  alpha1 = 0.05, alpha2 = 0.001, mu = 2)
+findClassyGenes(
+  expDat,
+  sampTab,
+  dLevel,
+  topX = 25,
+  dThresh = 0,
+  alpha1 = 0.05,
+  alpha2 = 0.001,
+  mu = 2
+)
 }
 \arguments{
 \item{expDat}{a matrix of normalized expression data from \code{\link{trans_prop}}}
diff --git a/man/hm_enr.Rd b/man/hm_enr.Rd
index ade51cb..0b9b070 100644
--- a/man/hm_enr.Rd
+++ b/man/hm_enr.Rd
@@ -4,8 +4,7 @@
 \alias{hm_enr}
 \title{heatmap of the enrichment result}
 \usage{
-hm_enr(esList, threshold = 0.05, cRows = FALSE, cCols = FALSE,
-  fsr = 4)
+hm_enr(esList, threshold = 0.05, cRows = FALSE, cCols = FALSE, fsr = 4)
 }
 \arguments{
 \item{esList}{returned from ks.extract.more}
diff --git a/man/hm_gpa_sel.Rd b/man/hm_gpa_sel.Rd
index 46dc258..5b708a6 100644
--- a/man/hm_gpa_sel.Rd
+++ b/man/hm_gpa_sel.Rd
@@ -4,9 +4,18 @@
 \alias{hm_gpa_sel}
 \title{heatmap genes and groups}
 \usage{
-hm_gpa_sel(expDat, genes, grps, maxPerGrp = 100, cRow = FALSE,
-  cCol = FALSE, limits = c(0, 10), toScale = FALSE,
-  fontsize_row = 4, reOrderCells = FALSE)
+hm_gpa_sel(
+  expDat,
+  genes,
+  grps,
+  maxPerGrp = 100,
+  cRow = FALSE,
+  cCol = FALSE,
+  limits = c(0, 10),
+  toScale = FALSE,
+  fontsize_row = 4,
+  reOrderCells = FALSE
+)
 }
 \arguments{
 \item{expDat}{expDat}
diff --git a/man/load10x.Rd b/man/load10x.Rd
index f3780ee..d03d54d 100644
--- a/man/load10x.Rd
+++ b/man/load10x.Rd
@@ -4,9 +4,15 @@
 \alias{load10x}
 \title{Loads 10x data mtx}
 \usage{
-load10x(path, prefix, mtx_fname = "matrix.mtx",
-  gene_fname = "genes.tsv", bc_fname = "barcodes.tsv",
-  bcFiltered = TRUE, removeRedundant = TRUE)
+load10x(
+  path,
+  prefix,
+  mtx_fname = "matrix.mtx",
+  gene_fname = "genes.tsv",
+  bc_fname = "barcodes.tsv",
+  bcFiltered = TRUE,
+  removeRedundant = TRUE
+)
 }
 \arguments{
 \item{path}{path}
diff --git a/man/makeGeneCompareTab.Rd b/man/makeGeneCompareTab.Rd
index a8d90e7..a5b2c08 100644
--- a/man/makeGeneCompareTab.Rd
+++ b/man/makeGeneCompareTab.Rd
@@ -4,8 +4,13 @@
 \alias{makeGeneCompareTab}
 \title{Make Gene Comparison Table}
 \usage{
-makeGeneCompareTab(queryExpTab, avgGeneTab, querySample = NULL,
-  trainingCat = NULL, geneSamples)
+makeGeneCompareTab(
+  queryExpTab,
+  avgGeneTab,
+  querySample = NULL,
+  trainingCat = NULL,
+  geneSamples
+)
 }
 \arguments{
 \item{queryExpTab}{a matrix of normalized expression query data from \code{\link{trans_prop}}}
diff --git a/man/mergeLoad10x.Rd b/man/mergeLoad10x.Rd
index bfb858e..7a6e4d7 100644
--- a/man/mergeLoad10x.Rd
+++ b/man/mergeLoad10x.Rd
@@ -4,8 +4,12 @@
 \alias{mergeLoad10x}
 \title{Loads 10x data mtx}
 \usage{
-mergeLoad10x(basePath, pNames, nCells = 1000,
-  secPath = "filtered_matrices_mex/hg19")
+mergeLoad10x(
+  basePath,
+  pNames,
+  nCells = 1000,
+  secPath = "filtered_matrices_mex/hg19"
+)
 }
 \arguments{
 \item{basePath}{path}
diff --git a/man/pca_to_tsne.Rd b/man/pca_to_tsne.Rd
index e1a7163..bf7118a 100644
--- a/man/pca_to_tsne.Rd
+++ b/man/pca_to_tsne.Rd
@@ -4,8 +4,7 @@
 \alias{pca_to_tsne}
 \title{make tsne from pca}
 \usage{
-pca_to_tsne(expDat, recRes, perplexity = 30, theta = 0.3,
-  weighted = TRUE)
+pca_to_tsne(expDat, recRes, perplexity = 30, theta = 0.3, weighted = TRUE)
 }
 \arguments{
 \item{expDat}{expDat}
diff --git a/man/plotGeneComparison.Rd b/man/plotGeneComparison.Rd
index 77417f7..4108de4 100644
--- a/man/plotGeneComparison.Rd
+++ b/man/plotGeneComparison.Rd
@@ -4,8 +4,15 @@
 \alias{plotGeneComparison}
 \title{Gene expression plotting}
 \usage{
-plotGeneComparison(expDat, grps, fontsize_row = 6, cRows = FALSE,
-  cCols = FALSE, toScale = FALSE, ...)
+plotGeneComparison(
+  expDat,
+  grps,
+  fontsize_row = 6,
+  cRows = FALSE,
+  cCols = FALSE,
+  toScale = FALSE,
+  ...
+)
 }
 \arguments{
 \item{expDat}{comparison expression matrix from \code{\link{makeGeneCompareTab}}}
diff --git a/man/ptGetTop.Rd b/man/ptGetTop.Rd
index 585f2a0..5ca2c09 100644
--- a/man/ptGetTop.Rd
+++ b/man/ptGetTop.Rd
@@ -4,8 +4,14 @@
 \alias{ptGetTop}
 \title{Find the best gene pairs for training}
 \usage{
-ptGetTop(expDat, cell_labels, cgenes_list = NA, topX = 50,
-  sliceSize = 5000, quickPairs = TRUE)
+ptGetTop(
+  expDat,
+  cell_labels,
+  cgenes_list = NA,
+  topX = 50,
+  sliceSize = 5000,
+  quickPairs = TRUE
+)
 }
 \arguments{
 \item{expDat}{expDat}
diff --git a/man/sc_Accu.Rd b/man/sc_Accu.Rd
index 07607bd..d1c0e5d 100644
--- a/man/sc_Accu.Rd
+++ b/man/sc_Accu.Rd
@@ -4,9 +4,14 @@
 \alias{sc_Accu}
 \title{Assess classifiers based on validation data}
 \usage{
-sc_Accu(ct_scores, stVal, dLevel = "description1",
-  dLevelSID = "sample_name", threshs = seq(0, 1, by = 0.005),
-  nRand = 50)
+sc_Accu(
+  ct_scores,
+  stVal,
+  dLevel = "description1",
+  dLevelSID = "sample_name",
+  threshs = seq(0, 1, by = 0.005),
+  nRand = 50
+)
 }
 \arguments{
 \item{ct_scores}{matrix of classification scores, rows = classifiers, columns = samples, colnames=sampleids}
diff --git a/man/sc_classAssess.Rd b/man/sc_classAssess.Rd
index 37943cf..ae96a0c 100644
--- a/man/sc_classAssess.Rd
+++ b/man/sc_classAssess.Rd
@@ -4,9 +4,18 @@
 \alias{sc_classAssess}
 \title{assess the classifiers performance based on validation data}
 \usage{
-sc_classAssess(stDat, washedDat, dLevel = "description1",
-  dLevelSID = "sample_name", minCells = 40, dThresh = 0,
-  propTrain = 0.25, nRand = 50, nTrees = 2000, resolution = 0.005)
+sc_classAssess(
+  stDat,
+  washedDat,
+  dLevel = "description1",
+  dLevelSID = "sample_name",
+  minCells = 40,
+  dThresh = 0,
+  propTrain = 0.25,
+  nRand = 50,
+  nTrees = 2000,
+  resolution = 0.005
+)
 }
 \arguments{
 \item{stDat}{sample table}
diff --git a/man/sc_hmClass.Rd b/man/sc_hmClass.Rd
index da1e1d0..d793981 100644
--- a/man/sc_hmClass.Rd
+++ b/man/sc_hmClass.Rd
@@ -4,8 +4,17 @@
 \alias{sc_hmClass}
 \title{heatmap of the classification result}
 \usage{
-sc_hmClass(classMat, grps, isBig = FALSE, maxPerGrp = 100,
-  cRow = FALSE, cCol = FALSE, fontsize_row = 4, scale = FALSE)
+sc_hmClass(
+  classMat,
+  grps,
+  isBig = FALSE,
+  maxPerGrp = 100,
+  cRow = FALSE,
+  cCol = FALSE,
+  fontsize_row = 8,
+  scale = FALSE,
+  label_reorder = TRUE
+)
 }
 \arguments{
 \item{classMat}{classMat}
diff --git a/man/sc_makeClassifier.Rd b/man/sc_makeClassifier.Rd
index b9b3710..e21591b 100644
--- a/man/sc_makeClassifier.Rd
+++ b/man/sc_makeClassifier.Rd
@@ -4,8 +4,15 @@
 \alias{sc_makeClassifier}
 \title{Make Classifier}
 \usage{
-sc_makeClassifier(expTrain, genes, groups, nRand = 70, ntrees = 2000,
-  stratify = FALSE, sampsize = 40)
+sc_makeClassifier(
+  expTrain,
+  genes,
+  groups,
+  nRand = 70,
+  ntrees = 2000,
+  stratify = FALSE,
+  sampsize = 40
+)
 }
 \arguments{
 \item{expTrain}{transformed training data from \code{\link{query_transform}}}
diff --git a/man/scn_extract_SN_DF.Rd b/man/scn_extract_SN_DF.Rd
index d086032..779cd58 100644
--- a/man/scn_extract_SN_DF.Rd
+++ b/man/scn_extract_SN_DF.Rd
@@ -4,8 +4,7 @@
 \alias{scn_extract_SN_DF}
 \title{returns a DF of: sample_id, description, ctt, subnet_name, score}
 \usage{
-scn_extract_SN_DF(scores, sampTab, dLevel, rnames = NULL,
-  sidCol = "sample_id")
+scn_extract_SN_DF(scores, sampTab, dLevel, rnames = NULL, sidCol = "sample_id")
 }
 \arguments{
 \item{scores}{a matrix of subNet scores}
diff --git a/man/scn_netScores.Rd b/man/scn_netScores.Rd
index e7eae55..c428027 100644
--- a/man/scn_netScores.Rd
+++ b/man/scn_netScores.Rd
@@ -4,8 +4,16 @@
 \alias{scn_netScores}
 \title{GRN status}
 \usage{
-scn_netScores(expDat, genes, tVals, ctt, classList = NULL,
-  classWeight = FALSE, exprWeight = TRUE, xmax = 1000)
+scn_netScores(
+  expDat,
+  genes,
+  tVals,
+  ctt,
+  classList = NULL,
+  classWeight = FALSE,
+  exprWeight = TRUE,
+  xmax = 1000
+)
 }
 \arguments{
 \item{expDat}{query expression matrix}
diff --git a/man/scn_score.Rd b/man/scn_score.Rd
index a841769..3ddbbe0 100644
--- a/man/scn_score.Rd
+++ b/man/scn_score.Rd
@@ -4,8 +4,16 @@
 \alias{scn_score}
 \title{GRN status}
 \usage{
-scn_score(expDat, subList, tVals, classList = NULL, minVals = NULL,
-  classWeight = FALSE, exprWeight = TRUE, xmax = 1000)
+scn_score(
+  expDat,
+  subList,
+  tVals,
+  classList = NULL,
+  minVals = NULL,
+  classWeight = FALSE,
+  exprWeight = TRUE,
+  xmax = 1000
+)
 }
 \arguments{
 \item{expDat}{query expression matrix}
diff --git a/man/scn_train.Rd b/man/scn_train.Rd
index f40fb38..0b3dfb1 100644
--- a/man/scn_train.Rd
+++ b/man/scn_train.Rd
@@ -4,10 +4,19 @@
 \alias{scn_train}
 \title{Training}
 \usage{
-scn_train(stTrain, expTrain, dLevel, colName_samp = "row.names",
-  nTopGenes = 10, nTopGenePairs = 25, nRand = 70, nTrees = 1000,
-  stratify = FALSE, weightedDown_total = 1500,
-  weightedDown_dThresh = 0.25, transprop_xFact = 10000)
+scn_train(
+  stTrain,
+  expTrain,
+  dLevel,
+  colName_samp = "row.names",
+  nTopGenes = 10,
+  nTopGenePairs = 25,
+  nRand = 70,
+  nTrees = 1000,
+  stratify = FALSE,
+  weightedDown_total = 10000,
+  weightedDown_dThresh = 0.25
+)
 }
 \arguments{
 \item{stTrain}{a dataframe that matches the samples with category}
@@ -28,9 +37,9 @@ scn_train(stTrain, expTrain, dLevel, colName_samp = "row.names",
 
 \item{weightedDown_dThresh}{the threshold at which anything lower than that is 0 for weighted_down function}
 
-\item{transprop_xFact}{scaling factor for transprop}
-
 \item{weightDown_total}{numeric post transformation sum of read counts for weighted_down function}
+
+\item{transprop_xFact}{scaling factor for transprop}
 }
 \value{
 a list containing normalized expression data, classification gene list, cnPRoc
diff --git a/man/scn_trainGRN.Rd b/man/scn_trainGRN.Rd
index 621fcca..9196d95 100644
--- a/man/scn_trainGRN.Rd
+++ b/man/scn_trainGRN.Rd
@@ -4,10 +4,19 @@
 \alias{scn_trainGRN}
 \title{Figure out normalization factors for GRNs, and norm training data}
 \usage{
-scn_trainGRN(expTrain, stTrain, subNets, classList = NULL,
-  dLevel = "description1", tVals = NULL, classWeight = FALSE,
-  exprWeight = FALSE, sidCol = "sample_id", xmax = 1000,
-  predSD = FALSE)
+scn_trainGRN(
+  expTrain,
+  stTrain,
+  subNets,
+  classList = NULL,
+  dLevel = "description1",
+  tVals = NULL,
+  classWeight = FALSE,
+  exprWeight = FALSE,
+  sidCol = "sample_id",
+  xmax = 1000,
+  predSD = FALSE
+)
 }
 \arguments{
 \item{expTrain}{expression matrix}
diff --git a/man/skylineClass.Rd b/man/skylineClass.Rd
index 99d0b93..0a9d50d 100644
--- a/man/skylineClass.Rd
+++ b/man/skylineClass.Rd
@@ -4,8 +4,15 @@
 \alias{skylineClass}
 \title{Skyline waterfall}
 \usage{
-skylineClass(classRes, cellType, sampTab, dLevel, yval,
-  cellIdLab = "cell_name", reorder = TRUE)
+skylineClass(
+  classRes,
+  cellType,
+  sampTab,
+  dLevel,
+  yval,
+  cellIdLab = "cell_name",
+  reorder = TRUE
+)
 }
 \arguments{
 \item{yval}{}
diff --git a/man/tsneMultsimp.Rd b/man/tsneMultsimp.Rd
index 896a047..06c63f9 100644
--- a/man/tsneMultsimp.Rd
+++ b/man/tsneMultsimp.Rd
@@ -4,9 +4,16 @@
 \alias{tsneMultsimp}
 \title{plot tsne and genes}
 \usage{
-tsneMultsimp(tsneDat, expDat, genesToPlot, colorPal = "BuPu",
-  revCol = TRUE, toScale = TRUE, limits = c(-3, 3),
-  themeWhite = TRUE)
+tsneMultsimp(
+  tsneDat,
+  expDat,
+  genesToPlot,
+  colorPal = "BuPu",
+  revCol = TRUE,
+  toScale = TRUE,
+  limits = c(-3, 3),
+  themeWhite = TRUE
+)
 }
 \arguments{
 \item{tsneDat}{tsne matrix}