v1.1.0 Plotting functions now exported.

BaderLab · Mar 2, 2019 · 9e90b7a · 9e90b7a
1 parent fe3a766
commit 9e90b7a
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Showing 29 changed files with 1,594 additions and 208 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -10,13 +10,30 @@ export(DEdist)
 export(DEdistNN)
 export(DEmarker)
 export(DEneighb)
+export(addCellMarkersToCGS)
+export(dotplotDEgenes)
+export(findKeyType)
 export(getEmb)
 export(getExpr)
 export(getMD)
+export(labelCellTypes)
+export(map2symbol)
 export(meanLogX)
+export(plot_GEboxplot)
+export(plot_clustSep)
+export(plot_clusterGenes_DEgenes)
+export(plot_clusterGenes_markers)
+export(plot_clusterGenes_search)
+export(plot_compareClusts)
+export(plot_deDotplot)
+export(plot_mdCompare)
+export(plot_mdPerClust)
+export(plot_sil)
+export(plot_tsne)
 export(rainbow2)
 export(runShiny)
 export(spreadLabels2)
+export(tsne_labels)
 exportClasses(sCVdata)
 exportClasses(sCVparams)
 exportMethods("ClustGeneStats<-")

diff --git a/R/deTest.R b/R/deTest.R
diff --git a/R/helperFx.R b/R/helperFx.R
@@ -85,6 +85,7 @@ cosineSim <- function(A,B) sum(A*B)/sqrt(sum(A^2)*sum(B^2))
 #' 
 #' @seealso \code{\link{map2symbol}}
 #' 
+#' @export
 
 findKeyType <- function(nge,annotationDB) {
   rownameKeytype <- "SYMBOL"
@@ -122,6 +123,7 @@ findKeyType <- function(nge,annotationDB) {
 #' @seealso \code{\link{findKeyType}},\code{\link[AnnotationDbi]{mapIds}},
 #'   \code{\link{addCellMarkersToCGS}}, and \code{\link{labelCellTypes}}.
 #' 
+#' @export
 
 map2symbol <- function(nge,annotationDB,rownameKeytype) {
   if (rownameKeytype != "SYMBOL") {
@@ -161,7 +163,8 @@ map2symbol <- function(nge,annotationDB,rownameKeytype) {
 #'
 #' @seealso \code{\link{findKeyType}}, \code{\link{map2symbol}}, and
 #'   \code{\link[AnnotationDbi]{mapIds}}.
-#' 
+#'   
+#' @export
 
 addCellMarkersToCGS <- function(sCV,cellMarkersU,cellMarkersS,symbolMap) {
   if (is.null(ClustGeneStats(sCV))) {
@@ -186,7 +189,7 @@ addCellMarkersToCGS <- function(sCV,cellMarkersU,cellMarkersS,symbolMap) {
 }
 
 
-#' Add predicted cell type names to cluster labels
+#' scClustViz helper fx: Add predicted cell type names to cluster labels
 #'
 #' A bare-bones method of predicting cell types from marker genes.
 #'
@@ -203,7 +206,8 @@ addCellMarkersToCGS <- function(sCV,cellMarkersU,cellMarkersS,symbolMap) {
 #' @return Returns the sCVdata object with an added attribute
 #'   '\code{ClusterNames}' to \code{Clusters(sCV)} containing the assigned cell
 #'   type names for each cluster.
-#'   
+#' 
+#' @export
 
 labelCellTypes <- function(sCV,cellMarkers,symbolMap) {
   if (length(cellMarkers) < 1) {