tanu/LSHTM_analysis
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split csv for isoniazid

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This commit is contained in:
Tanushree Tunstall 2021-09-20 16:12:45 +01:00
parent 5cd6c300a7
commit daa3556ede
3 changed files with 82 additions and 28 deletions
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1
dynamut/split_csv.sh
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@ -19,5 +19,6 @@ split ../../${INFILE} -l ${CHUNK} -d snp_batch_
#~/git/LSHTM_analysis/dynamut/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50
#~/git/LSHTM_analysis/dynamut/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50
#~/git/LSHTM_analysis/dynamut/split_csv.sh pnca_mcsm_formatted_snps.csv snp_batches 50
#~/git/LSHTM_analysis/dynamut/split_csv.sh katg_mcsm_formatted_snps.csv snp_batches 50 #Date: 20/09/2021
# add .txt to the files

107
my_header.R
View file

@ -1,21 +1,31 @@
#########################################################
### A) Installing and loading required packages
# A) Installing and loading required packages
# B) My functions
#########################################################
#########################################################
#lib_loc = "/usr/local/lib/R/site-library")
#if (!require("gplots")) {
# install.packages("gplots", dependencies = TRUE)
# library(gplots)
#}
require("getopt", quietly = TRUE) # cmd parse arguments
#if (!require("tidyverse")) {
# install.packages("tidyverse", dependencies = TRUE)
# library(tidyverse)
#}
if (!require("tidyverse")) {
install.packages("tidyverse", dependencies = TRUE)
library(tidyverse)
}
if (!require("ggplot2")) {
install.packages("ggplot2", dependencies = TRUE)
library(ggplot2)
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")) {
@ -23,6 +33,35 @@ if (!require("ggridges")) {
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)
@ -103,11 +142,6 @@ if (!require ("psych")){
library(psych)
}
if (!require ("dplyr")){
install.packages("dplyr")
library(dplyr)
}
if (!require ("compare")){
install.packages("compare")
library(compare)
@ -118,18 +152,37 @@ if (!require ("arsenal")){
library(arsenal)
}
if(!require(ggseqlogo)){
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)
}
library(protr)
if(!require(protr)){
install.packages("protr")
library(protr)
}
#if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#BiocManager::install("Logolas")
library("Logolas")
####################################
# 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!