--- a/macros_cheetah.xml	Wed Jan 29 17:16:36 2020 -0500
+++ b/macros_cheetah.xml	Thu Apr 15 18:58:21 2021 +0000
@@ -127,15 +127,19 @@
 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
 #end if
 
+cluster.compumap = formals(compumap)
 cluster.comptsne = formals(comptsne)
 cluster.compfr = formals(compfr)
 
 cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' )
 cluster.compfr\$knn = as.integer( '$tsne.knn' )
+cluster.compumap\$n_neighbors = as.integer( '$tsne.umap_nn' )
 #if str($tsne.use.def) == "no":
 cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' )
 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' )
 cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' )
+cluster.compumap\$n_epochs = as.integer( '$tsne.use.umap_epochs' )
+cluster.compumap\$min_dist = as.numeric( '$tsne.use.umap_min_dist' )
 #end if
 
 genelist.tablelim = as.integer( '$extra.tablelim' )
@@ -227,6 +231,7 @@
 perform.diffgene = TRUE
 plotdiffg\$Aname = '$diffgtest.set_a.name_set'
 plotdiffg\$Bname = '$diffgtest.set_b.name_set'
+plotdiffg\$... = NULL
 
 gfdat.A.use = list()
 gfdat.B.use = list()
@@ -294,7 +299,7 @@
 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' )
 pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' )
 #if str($plotgraph.use.def) == "no":
-pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' )
+##pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' )
 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' )
 #end if