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Commit b7c0e51e authored by Dhanaprakash Jambulingam's avatar Dhanaprakash Jambulingam
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Removed .RData and .Rhistory

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shiny::runApp('corplot')
shiny::runApp('corplot')
c
tumor_expression_plot_Christoffer <- read.delim("~/tumor_expression_plot_Christoffer.txt", row.names=1)
View(tumor_expression_plot_Christoffer)
cormat<-signif(cor(tumor_expression_plot_Christoffer),2)
cormat
View(cormat)
col<- colorRampPalette(c("blue", "white", "red"))(20)
heatmap(cormat, col=col, symm=TRUE)
cormat<-signif(cor(tumor_expression_plot_Christoffer),1)
View(cormat)
cormat<-signif(cor(1,tumor_expression_plot_Christoffer))
cormat<-signif(1,cor(tumor_expression_plot_Christoffer))
View(cormat)
cormat<-signif(cor(tumor_expression_plot_Christoffer))
View(cormat)
dist(tumor_expression_plot_Christoffer)
cor(tumor_expression_plot_Christoffer)
cor(tumor_expression_plot_Christoffer,2)
cor(tumor_expression_plot_Christoffer),2
cor(tumor_expression_plot_Christoffer)
runApp('corplot')
runApp('Downloads/shinyCorrplot-gh-pages')
shiny::runApp('corplot')
runApp('corplot')
runApp('corplot')
runApp('corplot')
runApp('corplot')
runApp('corplot')
runApp('corplot')
runApp('corplot')
shiny::runApp('corplot')
shiny::runApp('corplot')
shiny::runApp('corplot')
runApp('corplot')
shiny::runApp('corplot')
install.packages("h5")
shiny::runApp('corplot')
shiny::runApp('publication/corplot')
?cormat
?cormap2
shiny::runApp('publication/corplot')
shiny::runApp('publication/corplot')
?cormap2
runApp('publication/corplot')
library(coreheat)
?cormap2
shiny::runApp('publication/corplot')
runApp('publication/corplot')
?citation
citation(package = "ggcorrplot")
library(ggcorrplot)
install.packages("ggcorrplot")
library(ggcorrplot)
citation(package = "ggcorrplot")
install.packages("graphics")
install.packages("graphics")
install.packages("graphics")
install.packages("graphics")
install.packages("graphics")
library(graphics)
??graphics
?graphics
install.packages("dataSet")
install.packages("grDevices")
install.packages("grDevices")
install.packages("grDevices")
library(grDevices)
?grDevices
library(grid)
?grid
install.packages("dataset")
install.packages("altset")
q
quit
exit
citation()
citation(package = "ggally")
install.packages("ggally")
install.packages("GGally")
library(GGally)
citation(package = "GGally")
citation(package = "corrplot")
citation(package = "GGally")
citation()
citation(package = "ggcorrplot")
citation(package = "shiny")
library("coreheat")
?cormap2
shiny::runApp('publication/corplot')
library(corrplot)
library(coreheat)
?coreheat
library(coreheat)
?coreheat
library(heatmapGen2)
?heatmapGen2
.libPaths()
.libPaths()
myLibraryLocation <- .libPaths()[1]
cranPackages <- c("shinyBS", "shinythemes", "knitr", "rmarkdown", "shinyjs", "plyr", "RColorBrewer", "R.utils", "gdata", "data.table", "foreach", "ggplot2", "scales", "curl", "openssl", "httr", "Rcurl", "XML", "WGCNA")
sapply(cranPackages, install.packages, lib = myLibraryLocation)
bioConPackages <- c("AnnotationDbi", "biomaRt", "org.Hs.eg.db", "org.Mm.eg.db", "Heatplus", "genefilter", "impute", "preprocessCore", "Go.db")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(bioConPackages)
install.packages("/home/dhajam/publication/corplot/packages/coreheat_0.1.0_R_x86_64-pc-linux-gnu.tar.gz", repos = NULL, type="source")
library(coreheat)
install.packages('rsconnect')
rsconnect::setAccountInfo(name='biocpr',
token='D7412524543BF89B036143D3FB9F8A57',
secret='<SECRET>')
rsconnect::setAccountInfo(name='biocpr',
token='D7412524543BF89B036143D3FB9F8A57',
secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX')
rsconnect::setAccountInfo(name='biocpr',
token='D7412524543BF89B036143D3FB9F8A57',
secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX')
lucid$currentUser()
library(rsconnect)
rsconnect::setAccountInfo(name='biocpr',
token='D7412524543BF89B036143D3FB9F8A57',
secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX')
rsconnect::setAccountInfo(name='biocpr',
token='D7412524543BF89B036143D3FB9F8A57',
secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX')
shiny::runApp('publication/corplot')
runApp('publication/corplot')
runApp('publication/corplot')
runApp('/home/dhajam/publication/corplot')
library(rsconnect)
rsconnect::deployApp('/home/dhajam/publication/corplot')
shiny::runApp('publication/corplot')
shiny::runApp('publication/corplot')
rsconnect::deployApp('/home/dhajam/publication/corplot')
runApp('publication/corplot')
runApp('publication/corplot')
shiny::runApp()
runApp()
rsconnect::deployApp('/home/dhajam/publication/corplot')
rsconnect::deployApp('/home/dhajam/publication/corplot')
allPackages <- installed.packages()
allPackages <- allPackages[ is.na(allPackages[,4]), 1]
sapply(allPackages, remove.packages)
shiny::runApp()
runApp()
rsconnect::deployApp('/home/dhajam/publication/corplot')
install.packages("rsconnect")
install.packages("rsconnect")
rsconnect::deployApp('/home/dhajam/publication/corplot')
rsconnect::deployApp('/home/dhajam/publication/corplot')
rsconnect::deployApp('/home/dhajam/publication/corplot')
rsconnect::appDependencies('/home/dhajam/publication/corplot')
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
installed.packages()
devtools::install_github("cancer-genetics-utu/readR")
install
install.packages("devtools")
devtools::install_github("cancer-genetics-utu/readR")
rsconnect::deployApp('/home/dhajam/publication/corplot')
devtools::install_github("cancer-genetics-utu/medseqr")
devtools::install_github("cancer-genetics-utu/coreheat")
devtools::install_github("cancer-genetics-utu/genRal")
devtools::install_github("cancer-genetics-utu/heatmapGen")
devtools::install_github("cancer-genetics-utu/heatmapGen2")
devtools::install_github("cancer-genetics-utu/PAMhm")
cran_packages <- c("R.methodsS3", "R.oo", "R.utils", "RColorBrewer", "RCurl", "XML", "clipr", "cluster", "curl", "data.table","devtools", "digest", "foreach", "gdata", "ggplot2", "httr", "knitr", "openssl", "plyr", "rmarkdown", "scales", "shiny", "shinyBS", "shinyjs", "shinythemes", "WGCNA")
bio_packages <- c("AnnotationDbi", "Biobase", "BiocGenerics", "GO.db", "Heatplus", "IRanges", "S4Vectors", "biomaRt", "genefilter", "impute", "latticeExtra", "org.Hs.eg.db", "org.Mm.eg.db", "preprocessCore")
sapply(cran_packages, install.packages)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(bio_packages)
install.packages("impute")
BiocManager::install("impute")
install.packages("WGCNA")
rsconnect::deployApp('/home/dhajam/publication/corplot')
devtools::install_github("cancer-genetics-utu/readR")
devtools::install_github("cancer-genetics-utu/medseqr")
devtools::install_github("cancer-genetics-utu/coreheat")
devtools::install_github("cancer-genetics-utu/genRal")
devtools::install_github("cancer-genetics-utu/heatmapGen")
devtools::install_github("cancer-genetics-utu/heatmapGen2")
devtools::install_github("cancer-genetics-utu/PAMhm")
devtools::install_github("cancer-genetics-utu/medseqr")
rsconnect::deployApp('/home/dhajam/publication/corplot')
BiocManager::install("Heatplus")
rsconnect::deployApp('/home/dhajam/publication/corplot')
options(repos = BiocManager::repositories())
getOption("repos")
rsconnect::deployApp('/home/dhajam/publication/corplot')
options(repos="https://CRAN.R-project.org")
getOption("repos")
options(repos = BiocManager::repositories())
getOption("repos")
rsconnect::deployApp('/home/dhajam/publication/corplot')
options(repos = "https://CRAN.R-project.org")
getOption("repos")
options(repos = BiocManager::repositories())
rsconnect::deployApp('/home/dhajam/publication/corplot')
rsconnect/shinyapps.io/biocpr/corplot.dcf
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− 2
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......@@ -5,6 +5,6 @@ account: biocpr
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 2285412
bundleId: 3220865
bundleId: 4780472
url: https://biocpr.shinyapps.io/corplot/
when: 1591145681.80498
when: 1625226629.75996
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