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Dhanaprakash Jambulingam
BioCPR
Commits
b7c0e51e
Commit
b7c0e51e
authored
Jul 02, 2021
by
Dhanaprakash Jambulingam
Browse files
Removed .RData and .Rhistory
parent
4ea9f3c7
Changes
3
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.RData
deleted
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4ea9f3c7
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.Rhistory
deleted
100644 → 0
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4ea9f3c7
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
View file @
b7c0e51e
...
...
@@ -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: 1
591145681.80498
when: 1
625226629.75996
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