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A couple more R libs

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This commit is contained in:
Bryan Roessler
2024-08-04 19:51:10 -04:00
parent 2586984a62
commit f68ed9677d
1 changed files with 16 additions and 6 deletions
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22
workflow/qhtcp-workflow
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@@ -532,7 +532,7 @@ interactive_header() {
else else
for ((c=1; c<2; c++)); do # safe loop that only runs once for ((c=1; c<2; c++)); do # safe loop that only runs once
echo "Enter a comma-separated list of project numbers to analyze" 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 if [[ $response == 0 ]]; then
ask_pn && PROJECTS+=("${ADD_PROJECTS[@]}") ask_pn && PROJECTS+=("${ADD_PROJECTS[@]}")
else 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_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 depends_r=(BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2
plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown
plotly htmlwidgets) plotly htmlwidgets gplots gdata)
depends_bioc=(UCSC.utils org.Sc.sgd.db) depends_bioc=(UCSC.utils org.Sc.sgd.db)
[[ $1 == "--get-depends" ]] && return 0 # if we just want to read the depends vars [[ $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() { r_interactions() {
debug "Running: ${FUNCNAME[0]}" debug "Running: ${FUNCNAME[0]}"
cat <<-EOF cat <<-EOF
@@ -1678,7 +1683,11 @@ r_interactions() {
debug "$RSCRIPT $script" "$@" debug "$RSCRIPT $script" "$@"
"$RSCRIPT" "$script" \ "$RSCRIPT" "$script" \
"$1" \ "$1" \
"${@:2}" # optional arguments "$2" \
"$3" \
"${4:-"$APPS_DIR/r/SGD_features.tab"}" \
"${5:-5}" \
"${@:6}" # optional arguments
} }
@@ -1933,7 +1942,7 @@ get_studies() {
# See TODO in markdown # See TODO in markdown
initials="${USER:0:2}" initials="${USER:0:2}"
INITIALS=${initials^^} INITIALS=${initials^^}
empty_study=0 empty_study=1
# Find an Exp directory that does not exist # Find an Exp directory that does not exist
while [[ -d $QHTCP_PROJECT_DIR/Exp$empty_study ]]; do 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. 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 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") $(cat "$1")
EOF EOF
echo ""
# Allow user to add/edit the study info file # Allow user to add/edit the study info file
if ! ((YES)); then if ! ((YES)); then