A couple more R libs

workflow/qhtcp-workflow

@@ -532,7 +532,7 @@ interactive_header() {
     else
       for ((c=1; c<2; c++)); do # safe loop that only runs once
         echo "Enter a comma-separated list of project numbers to analyze"
-        ((YES)) || read -r -p "Or enter 0 to add a new project or hit Enter for default project # ($num): " response
+        ((YES)) || read -r -p "Or enter 0 to add a new project or hit Enter for default project($num): " response
         if [[ $response == 0 ]]; then 
           ask_pn && PROJECTS+=("${ADD_PROJECTS[@]}")
         else
@@ -644,7 +644,7 @@ install_dependencies() {
   depends_perl=(Test::Warnings Test::Fatal File::Map Sub::Uplevel ExtUtils::Config ExtUtils::PkgConfig IPC::Run Module::Build::Tiny IPC::Run GD GO::TermFinder)
   depends_r=(BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2 
     plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown
-    plotly htmlwidgets)
+    plotly htmlwidgets gplots gdata)
   depends_bioc=(UCSC.utils org.Sc.sgd.db)
 
   [[ $1 == "--get-depends" ]] && return 0 # if we just want to read the depends vars
@@ -1659,7 +1659,12 @@ submodule r_interactions
 #
 # *
 #
-# @arg $1 string The current working directory
+# @arg $1 string The input directory
+# @arg $2 string The study info file
+# @arg $3 string The zscores directory
+# @arg $4 string SGD_features.tab
+# @arg $5 integer delta SD background value (default: 5)
+
 r_interactions() {
   debug "Running: ${FUNCNAME[0]}"
   cat <<-EOF
@@ -1678,7 +1683,11 @@ r_interactions() {
   debug "$RSCRIPT $script" "$@"
   "$RSCRIPT" "$script" \
     "$1" \
-    "${@:2}" # optional arguments
+    "$2" \
+    "$3" \
+    "${4:-"$APPS_DIR/r/SGD_features.tab"}" \
+    "${5:-5}" \
+    "${@:6}" # optional arguments
 }
 
 
@@ -1933,7 +1942,7 @@ get_studies() {
   # See TODO in markdown
   initials="${USER:0:2}"
   INITIALS=${initials^^}
-  empty_study=0
+  empty_study=1
 
   # Find an Exp directory that does not exist
   while [[ -d $QHTCP_PROJECT_DIR/Exp$empty_study ]]; do
@@ -1954,10 +1963,11 @@ get_studies() {
 		Give each experiment labels to be used for the plots and specific files. 
 		Enter the desired Experiment names and order them in the way you want them to appear in the REMc heatmaps
 
-		Current StudyInfo file ($1) contents:
+		Current study info file ($1) contents:
 
 		$(cat "$1")
 	EOF
+  echo ""
 
   # Allow user to add/edit the study info file
   if ! ((YES)); then