diff --git a/.RData b/.RData new file mode 100644 index 0000000000000000000000000000000000000000..929ce29797a1ac33cd52ab858bd1ae9ed17de8f0 Binary files /dev/null and b/.RData differ diff --git a/.Rhistory b/.Rhistory new file mode 100644 index 0000000000000000000000000000000000000000..2aed2d46480910b29baa911033fad5b39146a869 --- /dev/null +++ b/.Rhistory @@ -0,0 +1,201 @@ +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') diff --git a/data/PrCaTCGASample.pdf b/data/PrCaTCGASample.pdf new file mode 100644 index 0000000000000000000000000000000000000000..78d283a6ff91d0274e7c418e00b5cf4814bf09fe Binary files /dev/null and b/data/PrCaTCGASample.pdf differ diff --git a/data/PrCaTCGASample.txt b/data/PrCaTCGASample.txt new file mode 100644 index 0000000000000000000000000000000000000000..134a5e4fcca81b9ec10a2176cbb9b576f040f38a --- /dev/null +++ b/data/PrCaTCGASample.txt @@ -0,0 +1,27 @@ +Hugo_Symbol TCGA-2A-A8VL-01 TCGA-2A-A8VO-01 TCGA-2A-A8VT-01 TCGA-2A-A8VV-01 TCGA-2A-A8W1-01 TCGA-2A-A8W3-01 TCGA-CH-5737-01 TCGA-CH-5738-01 TCGA-CH-5739-01 TCGA-CH-5740-01 TCGA-CH-5741-01 TCGA-CH-5743-01 TCGA-CH-5744-01 TCGA-CH-5746-01 TCGA-CH-5748-01 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1.2122 1.186 -0.601 -0.3212 1.3635 1.4605 1.1764 1.2944 1.0647 -0.8643 -0.7119 -0.3933 -0.6907 -0.799 1.0347 0.6231 1.0933 -0.6605 -0.7959 0.4488 0.9595 0.7079 1.2484 -0.8383 -1.2568 1.214 -0.9649 0.9265 -0.9084 1.011 -0.4505 -0.9441 -0.6101 1.2077 -0.6161 -1.1015 1.4062 -0.7251 1.4157 -1.3281 0.943 1.0204 -0.586 -0.5449 1.163 1.1894 -0.6946 0.6901 0.7786 -0.5744 1.2706 1.3335 1.1483 -0.9695 1.1097 1.0799 1.2218 -0.4676 1.0441 -0.7616 -0.0961 -0.7912 0.5132 0.7857 1.1869 -1.0103 1.1793 -0.9698 -1.0686 -0.497 -1.1608 1.2557 -0.6493 1.025 -0.8997 1.3348 1.4545 -0.7025 1.3436 -1.5453 1.2482 -0.7068 1.1497 -0.567 1.271 0.9329 0.6963 0.3946 1.0987 -0.0671 1.1517 -0.6947 1.0031 -1.1675 -1.4476 -0.579 1.0709 1.2649 -0.8305 -1.0255 -0.7954 -1.3092 -0.582 -0.8214 -0.9587 1.2321 -0.7625 -0.2171 -0.507 -0.6831 -0.7723 -0.9779 -0.3427 -0.9014 -0.8559 1.2195 -0.56 0.4545 -1.0874 -0.3807 0.8658 1.0799 -0.9759 -1.0804 -0.5544 1.0178 -0.7169 0.7171 1.2965 1.392 -0.2916 1.061 -0.8982 0.9522 1.6291 -0.5835 -1.0228 -1.164 1.4859 -0.9964 -1.3537 -1.3642 -1.1515 0.6731 0.1304 -1.3997 1.1947 -0.8379 -1.2317 1.3473 1.2149 1.5772 -1.1453 -0.534 -0.7821 -1.4803 1.3336 -0.6758 -1.0182 1.2579 -0.675 -0.6885 -0.6481 1.639 -0.753 1.105 -0.7089 -0.3753 -1.0791 -1.2057 -0.5854 -0.7816 -1.3315 -0.6531 0.8968 diff --git a/data/README.md b/data/README.md index 08cb03e73148651aab2be1946d5898e01eef75a7..e9db0d821d30623a24318afaa7911aa283a119ba 100644 --- a/data/README.md +++ b/data/README.md @@ -1,3 +1,3 @@ ### 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`. diff --git a/data/subset_GDS5072.tsv b/data/subset_GDS5072.tsv deleted file mode 100644 index 227a6b271dac80544c0358f383318d29b50c2d82..0000000000000000000000000000000000000000 --- a/data/subset_GDS5072.tsv +++ /dev/null @@ -1,19 +0,0 @@ -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 diff --git a/markdown/README.md b/markdown/README.md index 1ea15922a574494265fa28d86d99d4ccc15ff352..fd381b65ddbc5ac8c3c62dfcd28a19064ee85197 100755 --- a/markdown/README.md +++ b/markdown/README.md @@ -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. diff --git a/markdown/usage_instructions.pdf b/markdown/usage_instructions.pdf new file mode 100644 index 0000000000000000000000000000000000000000..c8da8f7e9b7825deea8dcccc07c76c0d5f8d125f Binary files /dev/null and b/markdown/usage_instructions.pdf differ diff --git a/rsconnect/shinyapps.io/biocpr/corplot.dcf b/rsconnect/shinyapps.io/biocpr/corplot.dcf new file mode 100644 index 0000000000000000000000000000000000000000..9665cde30ebc9911d47dee2ba07174b7bb35b767 --- /dev/null +++ b/rsconnect/shinyapps.io/biocpr/corplot.dcf @@ -0,0 +1,10 @@ +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 diff --git a/server.R b/server.R index 403b4a9de8ff6a552c5ce66aae8a7293f5add96e..e3ae9dbfbce3330869a4e35e577aa2947125dcad 100755 --- a/server.R +++ b/server.R @@ -1,18 +1,39 @@ ## 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) diff --git a/ui.R b/ui.R index 9598a284c18cff5a617b46d54a20d7c57cf680e6..e3fa648bb6e25c451ecb68682eb778334385dd0a 100755 --- a/ui.R +++ b/ui.R @@ -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.")))))) )