moved Header_TT.R from plotting/ to scripts

scripts/Header_TT.R

@@ -0,0 +1,190 @@
+#########################################################
+# A) Installing and loading required packages
+# B) My functions
+#########################################################
+
+#########################################################
+#lib_loc = "/usr/local/lib/R/site-library")
+
+require("getopt", quietly = TRUE) # cmd parse arguments
+
+if (!require("tidyverse")) {
+  install.packages("tidyverse", dependencies = TRUE)
+  library(tidyverse)
+}
+
+if (!require("shiny")) {
+  install.packages("shiny", dependencies = TRUE)
+  library(shiny)
+}
+
+if (!require("shinyBS")) {
+  install.packages("shinyBS", dependencies = TRUE)
+  library(shinyBS)
+}
+
+if (!require("gridExtra")) {
+  install.packages("gridExtra", dependencies = TRUE)
+  library(gridExtra)
+}
+
+if (!require("ggridges")) {
+  install.packages("ggridges", dependencies = TRUE)
+  library(ggridges)
+}
+
+# if (!require("ggplot2")) {
+#   install.packages("ggplot2", dependencies = TRUE)
+#   library(ggplot2)
+# }
+
+# if (!require ("dplyr")){
+#   install.packages("dplyr")
+#   library(dplyr)
+# }
+
+if (!require ("DT")){
+  install.packages("DT")
+  library(DT)
+}
+
+if (!require ("plyr")){
+   install.packages("plyr")
+   library(plyr)
+ }
+
+# Install
+#if(!require(devtools)) install.packages("devtools")
+#devtools::install_github("kassambara/ggcorrplot")
+
+if (!require ("ggbeeswarm")){
+   install.packages("ggbeeswarm")
+   library(ggbeeswarm)
+}
+
+if (!require("plotly")) {
+  install.packages("plotly", dependencies = TRUE)
+  library(plotly)
+}
+
+if (!require("cowplot")) {
+  install.packages("copwplot", dependencies = TRUE)
+  library(cowplot)
+}
+
+if (!require("ggcorrplot")) {
+  install.packages("ggcorrplot", dependencies = TRUE)
+  library(ggcorrplot)
+}
+
+if (!require("ggpubr")) {
+  install.packages("ggpubr", dependencies = TRUE)
+  library(ggpubr)
+}
+
+if (!require("RColorBrewer")) {
+  install.packages("RColorBrewer", dependencies = TRUE)
+  library(RColorBrewer)
+}
+
+if (!require ("GOplot")) {
+  install.packages("GOplot")
+  library(GOplot)
+}
+
+if(!require("VennDiagram")) {
+  install.packages("VennDiagram", dependencies = T)
+  library(VennDiagram)
+}
+
+if(!require("scales")) {
+  install.packages("scales", dependencies = T)
+  library(scales)
+}
+
+if(!require("plotrix")) {
+  install.packages("plotrix", dependencies = T)
+  library(plotrix)
+}
+
+if(!require("stats")) {
+  install.packages("stats", dependencies = T)
+  library(stats)
+}
+
+if(!require("stats4")) {
+  install.packages("stats4", dependencies = T)
+  library(stats4)
+}
+
+if(!require("data.table")) {
+install.packages("data.table")
+  library(data.table)
+}
+
+if (!require("PerformanceAnalytics")){
+  install.packages("PerformanceAnalytics", dependencies = T)
+  library(PerformaceAnalytics)
+}
+
+if (!require ("GGally")){
+  install.packages("GGally")
+  library(GGally)
+}
+
+if (!require ("corrr")){
+  install.packages("corrr")
+  library(corrr)
+}
+
+if (!require ("psych")){
+  install.packages("psych")
+  library(psych)
+}
+
+if (!require ("compare")){
+  install.packages("compare")
+  library(compare)
+}
+
+if (!require ("arsenal")){
+  install.packages("arsenal")
+  library(arsenal)
+}
+
+if(!require(ggseqlogo)){
+  install.packages("ggseqlogo")
+  library(ggseqlogo)
+}
+
+# for PDB files
+if(!require(bio3d)){
+  install.packages("bio3d")
+  library(bio3d)
+}
+
+library(protr)
+if(!require(protr)){
+  install.packages("protr")
+  library(protr)
+}
+
+#if (!requireNamespace("BiocManager", quietly = TRUE))
+#  install.packages("BiocManager")
+
+#BiocManager::install("Logolas")
+#library("Logolas")
+library("Biostrings")
+
+####################################
+# Load all my functions:
+# only works if tidyverse is loaded
+# hence included it here!
+####################################
+
+func_path = "~/git/LSHTM_analysis/scripts/functions/"
+source_files <- list.files(func_path, "\\.R$")  # locate all .R files
+map(paste0(func_path, source_files), source)  # source all your R scripts!
+
+# set plot script dir
+plot_script_path = "~/git/LSHTM_analysis/scripts/plotting/"