--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_cheetah.xml	Mon Aug 12 13:01:12 2019 -0400
@@ -0,0 +1,377 @@
+<macros>
+    <token name="@FILTNORM_CHEETAH@"><![CDATA[
+## Perform do.filter
+use.filtnormconf = TRUE
+
+## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
+use.cluster = FALSE
+
+in.table = read.table(
+    '${intable}',
+    stringsAsFactors = F,
+    na.strings=c("NA", "-", "?", "."),
+    sep='\t',
+    header=TRUE,
+    row.names=1
+)
+
+## Hidden flag to use test data instead
+## see: test-data/use.intestinal
+
+use.test.data = (names(in.table)[1] == "test")
+
+sc = NULL
+if (use.test.data) {
+  sc = SCseq(intestinalData)
+  message("Loading test data from library")
+} else {
+  sc = SCseq(in.table)
+}
+
+
+filt = formals(filterdata)
+filt.ccc = formals(CCcorrect)
+filt.use.ccorrect = FALSE
+filt.lbatch.regexes = NULL
+
+filt.geqone = as.logical( '$filt.hist_geq_one' )
+filt\$mintotal = as.integer( '$filt.mintotal' )
+filt\$minexpr = as.integer( '$filt.minexpr' )
+filt\$minnumber = as.integer( '$filt.minnumber' )
+#if str($filt.use.def) == "no":
+filt\$knn = as.integer( '$filt.use.knn' )
+filt\$ccor = as.numeric( '$filt.use.ccor' )
+filt\$bmode = as.character( '$filt.use.bmode' )
+    #if $filt.use.LBatch_regexes:
+filt.lbatch.regexes = string2textvector( '$filt.use.LBatch_regexes' )
+    #end if
+    #if $filt.use.CGenes:
+filt\$CGenes = string2textvector( '$filt.use.CGenes' )
+    #end if
+    #if $filt.use.FGenes:
+filt\$FGenes = string2textvector( '$filt.use.FGenes' )
+    #end if
+    #if str($filt.use.ccc.use) == "yes"
+filt.use.ccorrect = TRUE
+        #if $filt.use.ccc.vset:
+filt.ccc\$vset = string2textvector( '$filt.use.ccc.vset' )
+        #end if
+        #if $filt.use.ccc.ncomp:
+filt.ccc\$nComp = as.integer( '$filt.use.ccc.ncomp' )
+        #end if
+filt.ccc\$pvalue = as.numeric( '$filt.use.ccc.pvalue' )
+filt.ccc\$quant = as.numeric( '$filt.use.ccc.quant' )
+filt.ccc\$dimR = as.logical( '$filt.use.ccc.dimr' )
+filt.ccc\$mode = as.character( '$filt.use.ccc.mode.value' )
+filt.ccc\$logscale = as.logical( '$filt.use.ccc.logscale' )
+    #end if
+#end if
+
+out.pdf = '${outpdf}'
+out.rdat = '${outrdat}'
+out.table = '${outtable}'
+
+]]></token>
+    <token name="@CLUSTER_CHEETAH@"><![CDATA[
+
+in.rdat = readRDS('${inputrds}')
+
+sc = in.rdat
+
+## Perform do.filter
+use.filtnormconf = FALSE
+
+## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
+use.cluster = TRUE
+
+
+clust.compdist = formals(compdist)
+clust.clustexp = formals(clustexp)
+clust.compdist\$metric = as.character( '$clust.metric' )
+clust.clustexp\$FUNcluster = as.character( '$clust.funcluster' )
+
+#if str($clust.use.def) == "no":
+
+clust.compdist\$FSelect = as.logical( '$clust.use.fselect' )
+    #if $clust.use.knn:
+clust.compdist\$knn = as.integer( '$clust.use.knn' )
+    #end if
+clust.clustexp\$sat = as.logical( '$clust.use.sat' )
+    #if $clust.use.samp:
+clust.clustexp\$samp = as.integer( '$clust.use.samp' )
+    #end if
+    #if $clust.use.cln:
+clust.clustexp\$cln = as.integer( '$clust.use.cln' )
+clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' )
+clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
+##clust.clustexp\$rseed = as.integer( '$clust.use.rseed' )
+    #end if
+#end if
+
+outlier.use.randomforest = FALSE
+outlier.findoutliers = formals(findoutliers)
+outlier.clustheatmap = formals(clustheatmap)
+outlier.rfcorrect = formals(rfcorrect)
+
+outlier.findoutliers\$outminc = as.integer( '$outlier.outminc' )
+outlier.findoutliers\$outlg = as.integer( '$outlier.outlg' )
+outlier.rfcorrect\$final = as.logical( '$outlier.final' )
+
+#if str($outlier.use.def) == "no":
+    #if $outlier.use.nbtree:
+outlier.rfcorrect\$nbtree = as.integer( '$outlier.use.nbtree' )
+    #end if
+outlier.findoutliers\$probthr = as.numeric( '$outlier.use.probthr' )
+outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' )
+##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' )
+outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
+#end if
+
+cluster.comptsne = formals(comptsne)
+cluster.compfr = formals(compfr)
+
+cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' )
+cluster.compfr\$knn = as.integer( '$tsne.knn' )
+#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' )
+#end if
+
+genelist.tablelim = as.integer( '$extra.tablelim' )
+genelist.plotlim = as.integer( '$extra.plotlim' )
+genelist.foldchange = as.integer( '$extra.foldchange' )
+genelist.pvalue = as.numeric( '$extra.pvalue' )
+
+out.pdf = '${outpdf}'
+out.rdat = '${outrdat}'
+out.genelist = '${outgenelist}'
+out.assignments = '${outassignments}'
+out.log = '${outlog}'
+
+]]>
+    </token>
+    <token name="@INSPECTCLUSTERS_CHEETAH@"><![CDATA[
+in.rdat = readRDS('${inputrds}')
+
+perform.plotting = FALSE
+perform.symbolmap = FALSE
+perform.genesofinterest = FALSE
+perform.diffgene = FALSE
+
+#if str($plotgen.do_opt) == "yes":
+perform.plotting = TRUE
+plotting.cln = string2numericvector( '$plotgen.clusts_plot' )
+#end if
+
+#if str($plotsym.do_opt) == "yes":
+perform.symbolmap = TRUE
+plotsym = formals(plotsymbolsmap)
+plotsym.use.typeremoveregex = NULL
+plotsym.use.typeremoveregex.subselect = NULL
+plotsym.use.typeremoveregex = as.character( '$plotsym.types_regex' )
+    #if str($plotsym.use.def) == "no":
+plotsym\$fr = as.logical( '$plotsym.use.fr' )
+        #if $plotsym.use.subset_regex:
+plotsym.use.typeremoveregex.subselect = as.character( '$plotsym.use.subset_regex' )
+        #end if
+    #end if
+#end if
+
+#if str($gois.do_opt) == "yes":
+perform.genesofinterest = TRUE
+plotexp = formals(plotexpmap)
+plotmarkg = formals(plotmarkergenes)
+
+inspect.goi.use.genes = string2textvector( '$gois.inspect_goi_genes' )
+plotexp\$g = inspect.goi.use.genes
+plotmarkg\$genes = inspect.goi.use.genes
+
+    #if $gois.inspect_goi_cells:
+inspect.goi.use.cells = as.character( '$gois.inspect_goi_cells' )
+plotexp\$cells = inspect.goi.use.cells
+plotmarkg\$cells = inspect.goi.use.cells
+    #end if
+    #if str($gois.use.def) == "no":
+inspect.goi.use.imputed = as.logical( '$gois.use.inspect_goi_imputed' )
+plotexp\$imputed = inspect.goi.use.imputed
+plotmarkg\$imputed = inspect.goi.use.imputed
+        #if $gois.use.plotmarkg_cl
+plotmarkg\$cl = string2numericvector( '$gois.use.plotmarkg_cl' )
+        #end if
+        #if $gois.use.plotmarkg_cap
+plotmarkg\$cap = as.integer( '$gois.use.plotmarkg_cap' )
+        #end if
+        #if $gois.use.plotmarkg_flo
+plotmarkg\$flo = as.integer( '$gois.use.plotmarkg_flo' )
+        #end if
+        #if $gois.use.plotmarkg_samples
+plotmarkg\$samples = as.character( '$gois.use.plotmarkg_samples' )
+        #end if
+        #if $gois.use.plotexp_n
+plotexp\$n = as.character( '$gois.use.plotexp_n' )
+        #end if
+plotmarkg\$cthr = as.integer( '$gois.use.plotmarkg_cthr' )
+plotmarkg\$order.cells = as.logical( '$gois.use.plotmarkg_order_cells' )
+plotmarkg\$aggr = as.logical( '$gois.use.plotmarkg_aggr' )
+plotmarkg\$norm = as.logical( '$gois.use.plotmarkg_norm' )
+plotmarkg\$cluster_cols = as.logical( '$gois.use.plotmarkg_cluster_cols' )
+plotmarkg\$cluster_rows = as.logical( '$gois.use.plotmarkg_cluster_rows' )
+plotmarkg\$cluster_set = as.logical( '$gois.use.plotmarkg_cluster_set' )
+    #end if
+#end if
+
+#if str($diffgtest.do_opt) == "yes":
+plotdiffg = formals(plotdiffgenesnb)
+
+perform.diffgene = TRUE
+plotdiffg\$Aname = '$diffgtest.set_a.name_set'
+plotdiffg\$Bname = '$diffgtest.set_b.name_set'
+
+gfdat.A.use = list()
+gfdat.B.use = list()
+
+gfdat.A.use\$manual = NULL
+gfdat.A.use\$regex = NULL
+gfdat.A.use\$cln = NULL
+gfdat.B.use\$manual = NULL
+gfdat.B.use\$regex = NULL
+gfdat.B.use\$cln = NULL
+
+    #if str($diffgtest.set_a.meth.type) == "cln":
+gfdat.A.use\$cln = string2numericvector( '$diffgtest.set_a.meth.selector' )
+    #else if str($diffgtest.set_a.meth.type) == "regex":
+gfdat.A.use\$regex = as.character( '$diffgtest.set_a.meth.selector' )
+    #else if str($diffgtest.set_a.meth.type) == "manual":
+gfdat.A.use\$manual = string2textvector( '$diffgtest.set_a.meth.selector' )
+    #end if
+
+    #if str($diffgtest.set_b.meth.type) == "cln":
+gfdat.B.use\$cln = string2numericvector( '$diffgtest.set_b.meth.selector' )
+    #else if str($diffgtest.set_b.meth.type) == "regex":
+gfdat.B.use\$regex = as.character( '$diffgtest.set_b.meth.selector' )
+    #else if str($diffgtest.set_b.meth.type) == "manual":
+gfdat.B.use\$manual = string2textvector( '$diffgtest.set_b.meth.selector' )
+    #end if
+
+    #if str($diffgtest.use.def) == "no":
+plotdiffg\$pthr = as.numeric( '$diffgtest.use.plotdiffg_pthr' )
+plotdiffg\$padj = as.logical( '$diffgtest.use.plotdiffg_padj' )
+plotdiffg\$lthr = as.integer( '$diffgtest.use.plotdiffg_lthr' )
+plotdiffg\$show_names = as.logical( '$diffgtest.use.plotdiffg_show_names' )
+        #if $diffgtest.use.plotdiffg_mthr
+plotdiffg\$mthr = as.numeric( '$diffgtest.use.plotdiffg_mthr' )
+        #end if
+    #end if
+#end if
+
+out.pdf='${outpdf}'
+    ]]></token>
+    <token name="@TRAJECTORY_CHEETAH@"><![CDATA[
+
+in.rdat = readRDS('${inputrds}')
+
+pstc.projc = formals(projcells)
+pstc.projc\$knn = as.integer( '$projcell.knn' )
+pstc.projc\$cthr = as.integer( '$projcell.cthr' )
+#if str($projcell.use.def) == "no":
+pstc.projc\$nmode = as.logical( '$projcell.use.nmode' )
+pstc.projc\$fr = as.logical( '$projcell.use.fr' )
+#end if
+
+pstc.projb = formals(projback)
+pstc.projb\$pdishuf = as.integer( '$projback.pdishuf' )
+#if str($projback.use.def) == "no":
+pstc.projb\$fast = as.logical( '$projback.use.fast' )
+pstc.projb\$rseed = as.integer( '$projback.use.rseed' )
+#end if
+
+pstc.comppval = formals(comppvalue)
+pstc.comppval\$pthr = as.numeric( '$comppval.pthr' )
+pstc.comppval\$sensitive = as.logical( '$comppval.sensitive' )
+
+pstc.plotgraph = formals(plotgraph)
+pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' )
+pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' )
+#if str($plotgraph.use.def) == "no":
+pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' )
+pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' )
+#end if
+
+pstc.compscore = formals(compscore)
+pstc.compscore\$nn = as.integer( '$compscore.nn' )
+pstc.compscore\$scthr = as.numeric( '$compscore.scthr' )
+
+out.pdf='${outpdf}'
+out.rdat='${outrdat}'
+    ]]></token>
+    <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
+in.rdat = readRDS('${inputrds}')
+
+perform.stemID = FALSE
+perform.fateID = FALSE
+perform.fateID.sominspect = FALSE
+
+#if str($trjsid.basic.doit) == "yes"
+perform.stemID = TRUE
+trjsid.getproj = formals(getproj)
+
+trjsid.numdiffgenes = 10
+trjsid.getproj\$i = as.integer( '$trjsid.basic.i' )
+trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
+
+   #if str($trjsid.basic.use.def) == "no":
+
+trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
+trjsid.numdiffgenes = as.integer( '$trjsid.basic.use.ndiffgenes' )
+
+   #end if
+#end if
+
+#if str($trjfid.basic.doit) == "yes":
+perform.fateID = TRUE
+trjfid.cellsfrom = formals(cellsfromtree)
+trjfid.filterset = formals(filterset)
+trjfid.getsom = formals(getsom)
+trjfid.procsom = formals(procsom)
+trjfid.plotheat = list()
+
+trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' )
+    #if str($trjfid.basic.use.def) == "no":
+
+trjfid.filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' )
+trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
+trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' )
+trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
+trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' )
+trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
+trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
+trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
+trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
+    #end if
+
+    #if str($trjfid.basic.som.doit) == "yes":
+perform.fateID.sominspect = TRUE
+
+trjfidsomi = list()
+        #if str($trjfid.basic.som.use_genes.typer) == "genelist":
+trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
+        #else if str($trjfid.basic.som.use_genes.typer) == "cln":
+trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
+        #end if
+
+trjfidsomi.use.types = '$trjfid.basic.som.use_types'
+trjfidsomi\$name = '$trjfid.basic.som.title'
+
+        #if str($trjfid.basic.som.use.def) == "no":
+trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
+trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' )
+        #end if
+    #end if
+#end if
+
+out.pdf = '${outpdf}'
+out.diffgenes = '${outdiffgenes}'
+
+]]></token>
+</macros>