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graphs for PS lineage dist for all and dr muts

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Tanu 2020-01-22 10:12:09 +00:00
parent 3c20be5615
commit c1ea688c5c
4 changed files with 93 additions and 567 deletions
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31
mcsm_analysis/pyrazinamide/scripts/Header_TT.R
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@ -1,25 +1,31 @@
#########################################################
### A) Installing and loading required packages
#########################################################
#lib_loc = "/usr/local/lib/R/site-library")
#if (!require("gplots")) {
# install.packages("gplots", dependencies = TRUE)
# library(gplots)
#}
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("plotly")) {
install.packages("plotly", dependencies = TRUE)
library(plotly)
}
if (!require("cowplot")) {
install.packages("copwplot", dependencies = TRUE)
library(ggplot2)
library(cowplot)
}
if (!require("ggcorrplot")) {
@ -43,37 +49,33 @@ if (!require ("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")) {
library(stats4)
install.packages("data.table")
library(data.table)
}
if (!require("PerformanceAnalytics")){
@ -98,18 +100,17 @@ if (!require ("psych")){
if (!require ("dplyr")){
install.packages("dplyr")
library(psych)
library(dplyr)
}
if (!require ("compare")){
install.packages("compare")
library(psych)
library(compare)
}
if (!require ("arsenal")){
install.packages("arsenal")
library(psych)
library(arsenal)
}