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.Rhistory
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## Will install packages (if not already installed)
if (!require("ggplot2")){install.packages("ggplot2")} # for plotting tSNE graphs
if (!require("colorRamps")){install.packages("colorRamps")} # for colour scheme management
if (!require("ggthemes")){install.packages("ggthemes")} # for plot themes
if (!require("scales")){install.packages("scales")} # for re-scaling if necessary
## Load packages
library(ggplot2) # for plotting tSNE graphs
library(colorRamps) # for colour scheme management
library(ggthemes) # for plot themes
library(scales) # for re-scaling, only if necessary
### 1.1 - Install packages (if not already installed) from CRAN
## From CRAN (required)
if(!require('plyr')) {install.packages('plyr')}
if(!require('data.table')) {install.packages('data.table')}
if(!require('rstudioapi')) {install.packages('rstudioapi')}
if(!require('devtools')){install.packages("devtools")}
## From CRAN (required for clustering and tSNE)
if(!require('FlowSOM')) {install.packages('FlowSOM')} # for running FlowSOM ### POSSIBLY INSTALL FROM GITHUB
if(!require('Rtsne')) {install.packages("Rtsne")} # for running tSNE
## From CRAN (only required for plotting -- if installation unsuccessful, set Run_tSNEplots and Run_ClusterPlots to 0)
if (!require("ggplot2")){install.packages("ggplot2")} # for plotting tSNE graphs
if (!require("colorRamps")){install.packages("colorRamps")} # for colour scheme management
if (!require("ggthemes")){install.packages("ggthemes")} # for plot themes
if (!require("scales")){install.packages("scales")} # for re-scaling if necessary
## From Bioconductor (required)
if(!require('flowViz')) {source("https://bioconductor.org/biocLite.R")
biocLite('flowViz')}
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library('plyr')
library('data.table')
library('rstudioapi')
library('devtools')
library('FlowSOM') ###
library('Rtsne')
library('ggplot2')
library('colorRamps')
library('ggthemes')
library('scales')
library('flowCore') ###
library('Biobase')
library('flowViz') ### matrixStats
## From CRAN (required)
if(!require('plyr')) {install.packages('plyr')}
if(!require('data.table')) {install.packages('data.table')}
if(!require('rstudioapi')) {install.packages('rstudioapi')}
if(!require('devtools')){install.packages("devtools")}
## From CRAN (required for clustering and tSNE)
if(!require('FlowSOM')) {install.packages('FlowSOM')} # for running FlowSOM ### POSSIBLY INSTALL FROM GITHUB
if(!require('Rtsne')) {install.packages("Rtsne")} # for running tSNE
## From CRAN (only required for plotting -- if installation unsuccessful, set Run_tSNEplots and Run_ClusterPlots to 0)
if (!require("ggplot2")){install.packages("ggplot2")} # for plotting tSNE graphs
if (!require("colorRamps")){install.packages("colorRamps")} # for colour scheme management
if (!require("ggthemes")){install.packages("ggthemes")} # for plot themes
if (!require("scales")){install.packages("scales")} # for re-scaling if necessary
## From Bioconductor (required)
if(!require('flowViz')) {source("https://bioconductor.org/biocLite.R")
biocLite('flowViz')}
if(!require('flowCore')) {source("https://bioconductor.org/biocLite.R")
biocLite('flowCore')}
if(!require('Biobase')) {source("https://bioconductor.org/biocLite.R")
biocLite('Biobase')}
### 1.4 Load packages
library('plyr')
library('data.table')
library('rstudioapi')
library('devtools')
library('FlowSOM') ###
library('Rtsne')
library('ggplot2')
library('colorRamps')
library('ggthemes')
library('scales')
library('flowCore') ###
library('Biobase')
library('flowViz') ### matrixStats