modified bp with option for adding stats and boxplplots. Moved old one to redundant

scripts/plotting/Header_TT.R

@@ -3,12 +3,6 @@
 #########################################################
 #lib_loc = "/usr/local/lib/R/site-library")
 
-#if (!require("gplots")) {
-#  install.packages("gplots", dependencies = TRUE)
-#  library(gplots)
-#}
-require(extrafont)
-
 require("getopt", quietly = TRUE) # cmd parse arguments
 
 if (!require("tidyverse")) {
@@ -16,9 +10,23 @@ if (!require("tidyverse")) {
   library(tidyverse)
 }
 
-if (!require("ggplot2")) {
-  install.packages("ggplot2", dependencies = TRUE)
-  library(ggplot2)
+# if (!require("ggplot2")) {
+#   install.packages("ggplot2", dependencies = TRUE)
+#   library(ggplot2)
+# }
+
+# if (!require ("dplyr")){
+#   install.packages("dplyr")
+#   library(dplyr)
+# }
+
+# Install
+#if(!require(devtools)) install.packages("devtools")
+#devtools::install_github("kassambara/ggcorrplot")
+
+if (!require ("ggbeeswarm")){
+   install.packages("ggbeeswarm")
+   library(ggbeeswarm)
 }
 
 if (!require("plotly")) {
@@ -101,11 +109,6 @@ if (!require ("psych")){
   library(psych)
 }
 
-if (!require ("dplyr")){
-  install.packages("dplyr")
-  library(dplyr)
-}
-
 if (!require ("compare")){
   install.packages("compare")
   library(compare)
@@ -116,31 +119,25 @@ if (!require ("arsenal")){
   library(arsenal)
 }
 
+if(!require(ggseqlogo)){
+  install.packages("ggseqlogo")
+  library(ggseqlogo)
+}
 
-#if (!requireNamespace("BiocManager", quietly = TRUE))
-#  install.packages("BiocManager")
-
-#BiocManager::install("Logolas")
-library("Logolas")
-
-#install.packages("ggseqlogo")
-library(ggseqlogo)
-
-
-####TIDYVERSE
-# Install
-#if(!require(devtools)) install.packages("devtools")
-#devtools::install_github("kassambara/ggcorrplot")
-
-library(ggcorrplot)
-
-
-###for PDB files
-#install.packages("bio3d") 
+# for PDB files
 if(!require(bio3d)){
   install.packages("bio3d")
   library(bio3d)
 }
 
-#install.packages("protr")
 library(protr)
+if(!require(protr)){
+  install.packages("protr")
+  library(protr)
+}
+
+#if (!requireNamespace("BiocManager", quietly = TRUE))
+#  install.packages("BiocManager")
+
+#BiocManager::install("Logolas")
+library("Logolas")