# HG changeset patch
# User iuc
# Date 1555365346 14400
# Node ID 0fa80752a314d84e787b084ea1de8e1cc9c0e871
# Parent  1067189592812fc786497bedba515dbaaadfb781
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit d94b3b8a4c7cf8c604279eb1eea24d32b3868922

diff -r 106718959281 -r 0fa80752a314 macros_cluster.xml
--- a/macros_cluster.xml	Thu Feb 28 17:41:26 2019 -0500
+++ b/macros_cluster.xml	Mon Apr 15 17:55:46 2019 -0400
@@ -287,6 +287,7 @@
 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' )
diff -r 106718959281 -r 0fa80752a314 scripts/cluster.R
--- a/scripts/cluster.R	Thu Feb 28 17:41:26 2019 -0500
+++ b/scripts/cluster.R	Mon Apr 15 17:55:46 2019 -0400
@@ -1,5 +1,5 @@
 #!/usr/bin/env R
-VERSION = "0.3"
+VERSION = "0.4"
 
 args = commandArgs(trailingOnly = T)
 
@@ -28,6 +28,10 @@
     filt.lib <- log10(colSums(getfdata(sc)))
     filt.feat <- log10(colSums(getfdata(sc)>0))
 
+    if (filt.geqone){
+        filt.feat <- log10(colSums(getfdata(sc)>=1))
+    }
+
     br <- 50
     ## Determine limits on plots based on the unfiltered data
     ## (doesn't work, R rejects limits and norm data is too different to compare to exp data
@@ -124,11 +128,12 @@
 
         goi <- head(rownames(dg.goi.table), genelist.plotlim)
         print(plotmarkergenes(sc, goi))
-        print(do.call(mtext, c(paste("                               Cluster ",n), test)))  ## spacing is a hack
+        buffer <- paste(rep("", 36), collapse=" ")
+        print(do.call(mtext, c(paste(buffer, "Cluster ",n), test)))  ## spacing is a hack
         test$line=-1
-        print(do.call(mtext, c(paste("                               Sig. Genes"), test)))  ## spacing is a hack
+        print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test)))  ## spacing is a hack
         test$line=-2
-        print(do.call(mtext, c(paste("                               (fc > ", genelist.foldchange,")"), test)))  ## spacing is a hack
+        print(do.call(mtext, c(paste(buffer, "(fc > ", genelist.foldchange,")"), test)))  ## spacing is a hack
 
     })
     write.table(df, file=out.genelist, sep="\t", quote=F)
@@ -139,10 +144,10 @@
 if (use.filtnormconf){
     sc <- do.filter(sc)
     message(paste(" - Source:: genes:",nrow(sc@expdata),", cells:",ncol(sc@expdata)))
-    message(paste(" - Filter:: genes:",nrow(sc@ndata),", cells:",ncol(sc@ndata)))
+    message(paste(" - Filter:: genes:",nrow(getfdata(sc)),", cells:",ncol(getfdata(sc))))
     message(paste("         :: ",
-                  sprintf("%.1f", 100 * nrow(sc@ndata)/nrow(sc@expdata)), "% of genes remain,",
-                  sprintf("%.1f", 100 * ncol(sc@ndata)/ncol(sc@expdata)), "% of cells remain"))
+                  sprintf("%.1f", 100 * nrow(getfdata(sc))/nrow(sc@expdata)), "% of genes remain,",
+                  sprintf("%.1f", 100 * ncol(getfdata(sc))/ncol(sc@expdata)), "% of cells remain"))
 }
 
 if (use.cluster){
diff -r 106718959281 -r 0fa80752a314 test-data/intestinal.filter.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intestinal.filter.log	Mon Apr 15 17:55:46 2019 -0400
@@ -0,0 +1,4 @@
+Loading test data from library
+ - Source:: genes: 20268 , cells: 431
+ - Filter:: genes: 2089 , cells: 287
+         ::  10.3 % of genes remain, 66.6 % of cells remain
diff -r 106718959281 -r 0fa80752a314 test-data/matrix.filter.geqone.pdf
Binary file test-data/matrix.filter.geqone.pdf has changed