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