Commit 4ea9f3c7 authored by Dhanaprakash Jambulingam's avatar Dhanaprakash Jambulingam
Browse files

Added usage instructions file and updated example file information in 'data/README.md'

parent 21b577da
File added
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')
This diff is collapsed.
### Example dataset
Example datasets can be found at `biocpr\data\` or can be obtained from [gitlab](https://gitlab.utu.fi/biocpr/corplot/tree/master/Data). The datasets have been downloaded from GEO database (DataSet Record GDS5072) and formatted so that they can be used with BioCPR. For more information on the dataset format, please refer `FAQ`.
Example datasets can be found at `biocpr\data\` or can be obtained from [gitlab](https://gitlab.utu.fi/dhajam/biocpr/-/tree/master/data). The dataset has been downloaded from The Cancer Genome Atlas (TCGA) dataset consisting of [333 patients with primary prostate cancer](https://www.cbioportal.org/study/summary?id=prad_tcga_pub). The dataset was obtained via the cBioPortal for Cancer Genomics and a subset of the data was created to contain genes commonly associated with cancer. The subset named "PrCaTCGASample.txt" is provided in the data repository.For more information on the dataset format, please refer `FAQ`.
IDENTIFIER GSM1095883 GSM1095886 GSM1095877 GSM1095878 GSM1095879 GSM1095880 GSM1095881 GSM1095882 GSM1095884 GSM1095885
APC 787.8 783.3 508.8 635.1 603.3 535.8 686.2 677.5 516.9 919.9
ATM 41.7 6.6 26.5 80.7 34.2 133.1 75.9 4.4 10.2 32.5
BRAF 1440.4 2108.8 1061.8 868 1155.4 1438.9 2179.1 1065.3 999 14487.9
BRCA1 79.9 364.3 384.7 182.7 353.3 498.7 911 416.2 328.7 535.2
BRCA2 23 3.2 58.3 2.1 23.5 21.9 2.5 3.5 8.8 45.5
CHD1 1299.1 946.9 588.9 1135.2 1386.3 938.7 594.7 1070.7 82.4 875.4
GNAS-AS1 74.7 23.2 13.6 20.2 14.4 67.4 8.6 105.2 44.9 61.1
ISG15 455.2 11685.6 968.2 8783.9 414.9 7630.3 17259 11813.4 1009.4 441.2
KMT2D 40.6 1.9 82.5 49 11.9 30.8 11.7 8.9 11.8 4.4
MYC 5012.4 2449.9 2327.5 3745.1 2382.7 1218.8 1977.5 4913.6 3260.4 1374.3
PIK3CA 239.3 180.2 236.8 134.4 291 282.1 459.8 52 454.6 327.9
PIK3CB 2308.7 2341.6 4040.1 3848 3987.7 3738.5 2004.6 3553.1 3001.7 4471.4
PTEN 1424.4 1656.8 1729.7 1188.8 256.3 1595.2 1471.2 1637.1 2416.7 3078.1
RAF1 152.4 319.5 646.7 988.3 2248.6 731.3 326.9 647.3 218.4 255.9
RB1 2704.4 3149.6 1567.8 3025 2565.6 1861.8 1962.3 3355.1 1313.6 3976.5
RSPO2 39.5 3.9 3.5 14.1 1.6 10.7 6.7 12.5 3.5 7.5
SPOP 1720.9 1331.5 1805.3 1456.7 1256.4 1213 1907.2 1980 1985.4 988.1
TP53 779.7 784.5 490.4 207.5 548.6 364 377.3 426.8 594.8 333.3
......@@ -12,8 +12,8 @@ The source code and installation instructions can be obtained from [gitlab](http
### Required Software
BioCPR requires additional in-house R packages in-order to run. The required packages can be obtained from this [link](https://gitlab.utu.fi/dhajam/biocpr).
BioCPR requires additional in-house R packages in-order to run. The required packages can be obtained from this [link](https://gitlab.utu.fi/dhajam/biocpr/blob/master/packages) or can be installed from github.
### Frequently asked questions
Please refer to the [FAQ](https://gitlab.utu.fi/dhajam/biocpr/blob/master/Markdown/FAQ.md) here.
Please refer to the [FAQ](https://gitlab.utu.fi/dhajam/biocpr/blob/master/markdown/FAQ.md) here.
name: corplot
title:
username:
account: biocpr
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 2285412
bundleId: 3220865
url: https://biocpr.shinyapps.io/corplot/
when: 1591145681.80498
## Required libraries ##
# 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")
# bio_packages <- c("AnnotationDbi", "Biobase", "BiocGenerics", "GO.db", "Heatplus","impute", "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)
#
# BiocManager::install("Heatplus")
# install.packages("WGCNA")
# 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")
library(shiny)
library(shinyBS)
library(plyr)
library(RColorBrewer)
library(genefilter)
library(DT)
library(digest)
library(readR)
library(medseqr)
library(coreheat)
library(genRal)
library(heatmapGen)
library(heatmapGen2)
library(genefilter)
library(DT)
library(PAMhm)
library(coreheat)
library(digest)
options(shiny.maxRequestSize = 40 * 1024 ^ 2)#increase maximum upload size for fileInput() to 40 MB
options(shiny.maxRequestSize = 52 * 1024 ^ 2)#increase maximum upload size for fileInput() to 40 MB
#library(shinysky)
......
......@@ -104,15 +104,15 @@ navbarPage(
tabPanel("About",
h4("About"),
hr(),
includeMarkdown("Markdown/README.md")),
includeMarkdown("markdown/README.md")),
tabPanel("FAQ",
h4("Frequently Asked Quesitons"),
hr(),
includeMarkdown("Markdown/FAQ.md")),
includeMarkdown("markdown/FAQ.md")),
tabPanel("Session Information",
h4("R session information"),
hr(),
includeMarkdown("Markdown/RSessionInfo.Rmd"))
includeMarkdown("markdown/RSessionInfo.Rmd"))
),
id='mainNavbarPage', footer=list(tags$hr(), tags$table(style="width: 100%; ", tags$tbody(tags$tr(tags$th(style="text-align: center; ", tags$label(style="font-family: Verdana; font-size: 12pt; font-weight: normal; color: grey; ", "This app has been created and is maintained by the Institute of Biomedicine, University of Turku."))))))
)
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