ylab="Width-normalized Pearson correlation",
xlim=c(0,1), ylim=c(0,1))
grid()
plot(oct4.tfbm.compa$cor,oct4.tfbm.compa$Ncor,
main="Effect of normalization on motif correlation",
xlab="Pearson correlation",
ylab="Width-normalized Pearson correlation",
)
grid()
xlim=c(-1,1), ylim=c(-1,1)
plot(oct4.tfbm.compa$cor,oct4.tfbm.compa$Ncor,
main="Effect of normalization on motif correlation",
xlab="Pearson correlation",
ylab="Width-normalized Pearson correlation",
xlim=c(-1,1), ylim=c(-1,1)
)
grid()
abline(h=0)
plot(oct4.tfbm.compa$cor,oct4.tfbm.compa$Ncor,
main="Effect of normalization on motif correlation",
xlab="Pearson correlation",
ylab="Width-normalized Pearson correlation",
xlim=c(-1,1), ylim=c(-1,1),col="blue"
)
grid()
abline(h=0)
abline(v=0)
abline(v=1)
abline(v=seq(from=-1,to=1,by=0.2))
abline(v=0)
plot(oct4.tfbm.compa$cor,oct4.tfbm.compa$Ncor,
main="Effect of normalization on motif correlation",
xlab="Pearson correlation",
ylab="Width-normalized Pearson correlation",
xlim=c(-1,1), ylim=c(-1,1),col="blue"
)
grid()
abline(h=0)
abline(v=0)
abline(v=0)
abline(a=0,b=1)
library(TFBMclust)
grid()
library(TFBMclust)
library(TFBMclust)
system("python /no_backup/rsat/python-scripts/gene2reaction_from_genoscope.py")
system("python /no_backup/rsat/python-scripts/random-motif")
system("python /no_backup/rsat/python-scripts/random-motif")
load("/no_backup/rsat/R-scripts/TFBMclust/.RData")
library(TFBMclust)
help(TFBMclust)
library(TFBMclust)
data(oct4chipseq)
data(oct4.tfbm.compa)
data
data()
data(oct4chipseq)
View(oct4.tfbm.compa)
View(oct4.tfbm.compa)
View(oct4.tfbm.desc)
View(oct4.tfbm.desc)
View(oct4.tfbm.compa)
View(oct4.tfbm.compa)
?View
library(TFBMclust)
data(oct4chipseq)
View(oct4.tfbm.compa)
View(oct4.tfbm.desc)
View(oct4.tfbm.desc)
library(TFBMclust)
?vignette
vignette(TFBMclust)
vignette(TFBMclust::align.leaf.and.cluster)
vignette(package=TFBMclust)
library(TFBMclust)
vignette(package="TFBMclust")
vignette(package="TFBMclust")
vignette(package="TFBMclust-package")
vignette("TFBMclust-package")
vignette("TFBMclust-package)
""
)
))
`
""
vignette("TFBMclust-package")
vignette("TFBMclust")
library(TFBMclust)
install.packages(c("manipulate", "mgcv"))
install.packages("knitr")
required.packages <- c("gplots",
"ctc",
"RJSONIO",
"dendextend",
"devtools",
"Rclusterpp")
for (package in required.packages) {
if(!require(package)){
install.packages(package, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
}
}
## Check requirement for other R packages
required.packages <- c("gplots",
"ctc",
"RJSONIO",
"dendextend",
"devtools",
"Rclusterpp")
for (package in required.packages) {
if(!require(package)){
print(paste("Installing package", package))
install.packages(package, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
}
}
for (package in required.packages) {
if(!require(get(package))){
print(paste("Installing package", package))
install.packages(get(package), repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
}
}
for (pkg in required.packages) {
if(!require(pkg)){
print(paste("Installing package", pkg))
install.packages(pkg, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
}
}
install.packages("ctc")
install.packages("dendextend")
library(Rclusterpp)
?require
for (pkg in required.packages) {library(pkg)}
for (pkg in required.packages) {library(get(pkg)}
for (pkg in required.packages) {library(pkg)}
required.packages
library(gplots)
get(pkg)
library(pkg)
library(get(pkg))
pkg
required.packages
get("RJSONIO")
get(RJSONIO)
library(RJSONIO)
library(dendextend)
required.packages
library(Rclusterpp)
library(ctc)
## Check requirement for bioconductor packages
bioconductor.packages <- c("ctc")
for (pkg in bioconductor.packages) {
if (!require(pkg)) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite(pkg)
}
}
bioclite(ctc)
biocLite(ctc)
biocLite("ctc")
biocLite(pkg)
pkg
bioconductor.packages <- c("ctc")
for (pkg in bioconductor.packages) {
if (!require(pkg)) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite(pkg)
}
}
bioconductor.packages <- c("ctc")
for (pkg in bioconductor.packages) {
if (!require(pkg)) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite(pkg)
library(pkg)
}
}
## Check requirement for other R packages
required.packages <- c("gplots",
"RJSONIO",
"dendextend",
"devtools",
"Rclusterpp")
for (pkg in required.packages) {
if(!require(pkg)){
print(paste("Installing package", pkg))
install.packages(pkg, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(pkg)
}
}
install.packages(pkg, repos = "http://cran.univ-lyon1.fr/", dependencies = TRUE)
if (!require("ctc")) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite("ctc")
library("ctc")
}
if (!require("ctc")) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite("ctc")
library("ctc")
}
if (!require("ctc")) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite("ctc")
library("ctc")
}
for pkg in (required.packages) {
print(paste("Loading package", pkg))
if(!require(pkg)){
print(paste("Installing package", pkg))
install.packages(pkg, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(pkg)
}
}
for pkg in (required.packages) {
print(paste("Loading package", pkg))}
for (pkg in required.packages) {
print(paste("Loading package", pkg))
}
for (pkg in required.packages) {
print(paste("Loading package", pkg))
if(!require(pkg)){
print(paste("Installing package", pkg))
}
}
for (pkg in required.packages) {
print(paste("Loading package", pkg))
to.load <- pkg
if(!require(to.load)){
print(paste("Installing package", pkg))
}
}
to.load <- pkg
to.load
if(!require(get(to.load)){
if(!require(get(to.load))){
print(paste("Installing package", pkg))
}
if(!require(get(to.load))){
print(paste("Installing package", pkg))
}
for (pkg in required.packages) {
print(paste("Loading package", pkg))
if(!require(pkg)) {
print(paste("Installing package", pkg))
}
}
if(!require(gplots)) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(gplots)
}
if(!require(gplots)) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(gplots)
}
if(!require(gplots)) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(gplots)
}
if(!require(gplots)) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(gplots)
}
if(!require("gplots")) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(gplots)
}
}
if(!require("gplots")) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(gplots)
}
if(!require("gplots")) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library("gplots")
}
if(!require("gplots")) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library("gplots")
}
for (pkg in required.packages) {
if(!require(pkg)) {
install.packages(pkg, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(pkg)
}
}
install.packages(pkg, repos = "http://cran.univ-lyon1.fr/", dependencies = TRUE)
required.packages <- c("gplots",
"RJSONIO",
"dendextend",
"devtools",
"Rclusterpp")
for (pkg in required.packages) {
if(!require(pkg)) {
install.packages(pkg, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(pkg)
}
}
pkg
if(!require("gplots")) {
install.packages("gplots", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library("gplots")
}
if(!require("RJSONIO")) {
install.packages("RJSONIO", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library("RJSONIO")
}
if(!require("dendextend")) {
install.packages("dendextend", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library("dendextend")
}
if(!require("devtools")) {
install.packages("devtools", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library("devtools")
}
if(!require("Rclusterpp")) {
install.packages("Rclusterpp", repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library("Rclusterpp")
}
required.packages <- c("gplots",
"RJSONIO",
"dendextend",
"devtools",
"Rclusterpp")
for (pkg in required.packages) {
if(!require(pkg)) {
install.packages(pkg, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(pkg)
}
}
?library
?getOption
?setOption
options
options()
options("verbos")
options("verbose")
options("verbose") <- FALSE
?library
required.packages <- c("gplots",
"RJSONIO",
"dendextend",
"devtools",
"Rclusterpp")
for (pkg in required.packages) {
if(!require(pkg, quietly=TRUE, character.only = TRUE)) {
install.packages(pkg, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(pkg, quietly=TRUE)
}
}
## generated by compare-matrices), performs hierarchical
## clustering.
##
## It returns the resulting tree in json format, which can be loaded
## by the d3 library for display purposes.
## Redefine the main directory (this should be adapted to local configuration)
dir.main <- getwd()
dir.rsat <- Sys.getenv("RSAT")
if (dir.rsat == "") {
stop("The environment variable RSAT is not defined.")
}
## Require TFBMclust if it is required
if(!require("TFBMclust")){
install.packages(file.path(dir.rsat, 'R-scripts/TFBMclust'), repos=NULL, type="source", dependencies=TRUE)
}
## Check requirement for other R packages
required.packages <- c("gplots",
"RJSONIO",
"dendextend",
"devtools",
"Rclusterpp")
for (pkg in required.packages) {
if(!require(pkg, quietly=TRUE, character.only = TRUE)) {
install.packages(pkg, repos="http://cran.univ-lyon1.fr/", dependencies=TRUE)
library(pkg, quietly=TRUE, character.only = TRUE)
}
}
## Check requirement for bioconductor packages
if (!require("ctc", quietly=TRUE)) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite("ctc")
library("ctc", quietly=TRUE)
}
## Load required libraries
for (pkg in c(required.packages, bioconductor.packages)) {
suppressPackageStartupMessages(library(pkg, warn.conflicts=FALSE, character.only = TRUE))
}
bioconductor.packages <- c("ctc")
for (pkg in bioconductor.packages) {
if (!require(pkg, quietly=TRUE, character.only = TRUE)) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite(pkg)
#  library("ctc", quietly=TRUE, character.only = TRUE)
}
}
bioconductor.packages <- c("ctc")
for (pkg in bioconductor.packages) {
if (!require(pkg, quietly=TRUE, character.only = TRUE)) {
source("http://bioconductor.org/biocLite.R")
biocLite();
biocLite(pkg)
#  library("ctc", quietly=TRUE, character.only = TRUE)
}
}
## Load required libraries
for (pkg in c(required.packages, bioconductor.packages)) {
suppressPackageStartupMessages(library(pkg, warn.conflicts=FALSE, character.only = TRUE))
}
??vignette
openVignette()
library(BioBase)
library(openvignette)
openVignette(package=NULL)
openVignette(package="TFBMclust")
library("TFBMclust")
openVignette(package="TFBMclust")
library(utils)
openVignette(package="TFBMclust")
vignette
vignette(package="TFBMclust")
vignette(package="TFBMclust")
library(TFBMclust)
vignette(package="TFBMclust")
?install.packages
dir.rsat.rlib <- file.path(dir.rsat, "R-scripts", "Rpackages")
dir.create(dir.rsat.rlib, recursive=TRUE,showWarnings=FALSE)
dir.rsat.rlib <- file.path(dir.rsat, "R-scripts", "Rpackages")
dir.create(dir.rsat.rlib, recursive=TRUE,showWarnings=FALSE)
install.packages(file.path(dir.rsat, 'R-scripts/TFBMclust'),
repos=NULL, type="source",
dependencies=TRUE,
lib=dir.rsat.rlib)
?require
dir.rsat.rlib <- file.path(dir.rsat, "R-scripts", "Rpackages")
dir.rsat.rlib <- file.path(dir.rsat, "R-scripts", "Rpackages")
if(!require("TFBMclust", lib.loc=dir.rsat.rlib)){
dir.create(dir.rsat.rlib, recursive=TRUE,showWarnings=FALSE)
install.packages(file.path(dir.rsat, 'R-scripts/TFBMclust'),
repos=NULL, type="source",
dependencies=TRUE,
lib=dir.rsat.rlib)
}
dir.rsat.rlib <- file.path(dir.rsat, "R-scripts", "Rpackages")
dir.create(dir.rsat.rlib, recursive=TRUE,showWarnings=FALSE)
if(!require("TFBMclust", lib.loc=dir.rsat.rlib)){
install.packages(file.path(dir.rsat, 'R-scripts/TFBMclust'),
repos=NULL, type="source",
dependencies=TRUE,
lib=dir.rsat.rlib)
}
install.packages(file.path(dir.rsat, 'R-scripts/TFBMclust'),
repos=NULL, type="source",
dependencies=TRUE,
lib=dir.rsat.rlib)
??environment
?system
?sysenv
??sysen
??sys
Sys.getenv("HOME")
dir.rsat.rlib <- file.path(dir.rsat, "R-scripts", "Rpackages")
dir.create(dir.rsat.rlib, recursive=TRUE,showWarnings=FALSE)
if(!require("TFBMclust", lib.loc=dir.rsat.rlib)){
install.packages(file.path(dir.rsat, 'R-scripts/TFBMclust'),
repos=NULL, type="source",
dependencies=TRUE,
lib=dir.rsat.rlib)
}
dir.rsat.rscripts <- file.path(dir.rsat, "R-scripts")
require("TFBMclust", lib.loc=dir.rsat.rscripts)
dir.rsat.rscripts <- file.path(dir.rsat, "R-scripts")
library("TFBMclust", lib.loc=dir.rsat.rscripts)
library("TFBMclust", lib.loc="boum")
dir.rsat.rscripts <- file.path(dir.rsat, "R-scripts")
library("TFBMclust", lib.loc=dir.rsat.rscripts)
getOption("repos")
?install.packages
library(TFBMclust)
?install.packages
install.packags(pkgs=file.path(dir.rsat.rscripts, "TFBMclust"), lib=dir.rsat.rlib, type="source")
install.packages(pkgs=file.path(dir.rsat.rscripts, "TFBMclust"), lib=dir.rsat.rlib, type="source")
install.packages(pkgs=file.path(dir.rsat.rscripts, "TFBMclust"), lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
install.packages(pkgs=file.path("TFBMclust", repos=dir.rsat.rscripts,  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
install.packages(pkgs="TFBMclust", repos=dir.rsat.rscripts,  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
#system(paste("R CMD INSTALL --no-multiarch --with-keep.source  \"", file.path(dir.rsat, "R-scripts/TFBMclust"), "\"", sep =""))
reload(file.path(dir.rsat, "R-scripts/TFBMclust"))
install.packages(pkgs="TFBMclust", repos=dir.rsat.rscripts,  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
install.packages(pkgs="TFBMclust", repos=dir.rsat.rscripts,  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
install.packages(pkgs = "TFBMclust", repos = dir.rsat.rscripts,
)
install.packages(pkgs="TFBMclust", repos=dir.rsat.rscripts,  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
install.packages(pkgs="TFBMclust", repos=file(dir.rsat.rscripts, "TFBMclust"),  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
install.packages(pkgs="TFBMclust", repos=file.path(dir.rsat.rscripts, "TFBMclust"),  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
install.packages(pkgs=file.path(dir.rsat.rscripts, "TFBMclust"), repos=NULL,  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
install.packages(pkgs=file.path(dir.rsat.rscripts, "TFBMclust"), repos=NULL,  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
reload(file.path(dir.rsat, "R-scripts/TFBMclust"))
suppressPackageStartupMessages(library(TFBMclust, warn.conflicts=FALSE))
reload(file.path(dir.rsat, "R-scripts/TFBMclust"))
?reload
install.packages(pkgs=file.path(dir.rsat.rscripts, "TFBMclust"), repos=NULL,  lib=dir.rsat.rlib, type="source", INSTALL_opts=c("no-multiarch"))
source('/no_backup/rsat/R-scripts/install_packages_for_rsat.R', echo=TRUE)
for (pkg in required.packages) {
#  if(!suppressPackageStartupMessages(require(pkg, quietly=TRUE, character.only = TRUE))) {
install.packages(pkg, repos="http://cran.rstudio.com/", dependencies=TRUE, lib=dir.rsat.rlib)
#  }
}
