Break out plot filtering

qhtcp-workflow/qhtcp-workflow

@@ -614,41 +614,6 @@ interactive_header() {
 module install_dependencies
 # @description This module will automatically install the dependencies for running QHTCP.
 #
-# If you wish to install them manually, you can use the following information to do so:
-#
-# #### System dependencies
-#
-# * R
-# * Perl
-# * Java
-# * MATLAB
-#
-# #### MacOS
-#
-# * `export HOMEBREW_BREW_GIT_REMOTE=https://github.com/Homebrew/brew`
-# * `/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"`
-# * `cpan File::Map ExtUtils::PkgConfig GD GO::TermFinder`
-# * `brew install graphiz gd pdftk-java pandoc shdoc nano rsync coreutils`
-#
-# #### Linux DEB
-#
-# * `apt install graphviz pandoc pdftk-java libgd-dev perl shdoc nano rsync coreutils libcurl-dev openssl-dev`
-#
-# #### Linux RPM
-#
-# * `dnf install graphviz pandoc pdftk-java gd-devel perl-CPAN shdoc nano rsync coreutils libcurl-devel openssl-devel`
-#
-# #### Perl
-#
-# * `cpan -I -i File::Map ExtUtils::PkgConfig GD GO::TermFinder`
-#
-# #### R
-#
-# * `install.packages(c('BiocManager', 'ontologyIndex', 'ggrepel', 'tidyverse', 'sos', 'openxlsx', 'ggplot2', 'plyr', 'extrafont', 'gridExtra', 'gplots', 'stringr', 'plotly', 'ggthemes', 'pandoc', 'rmarkdown', 'plotly', 'htmlwidgets'), dep=TRUE)`
-# * `BiocManager::install('UCSC.utils')`
-# * `BiocManager::install('org.Sc.sgd.db')`
-#
-#
 install_dependencies() {
   debug "Running: ${FUNCNAME[0]} $*"
 
@@ -669,8 +634,8 @@ install_dependencies() {
     ExtUtils::PkgConfig IPC::Run Module::Build::Tiny GD GO::TermFinder)
   depends_r=(
     BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2 
-    plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc
-    rmarkdown plotly htmlwidgets gplots gdata Hmisc)
+    dplyr rlang data.table unix gridExtra gplots stringr plotly ggthemes pandoc
+    rmarkdown htmlwidgets gdata Hmisc)
   depends_bioc=(UCSC.utils org.Sc.sgd.db)
 
   [[ $1 == "--get-depends" ]] && return 0 # if we just want to read the depends vars