Augustin Luna cannin
cannin
/ RunColorExistingCytoscapeNetworkExample.R
Last active
August 29, 2015 14:02
An example of programmatically coloring nodes/edges of an existing Cytoscape network with R
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| # An example of programmatically coloring nodes/edges of an existing Cytoscape network with R | |
| library(RCytoscape) | |
| library(RColorBrewer) | |
| # Generate demo Cytoscape network | |
| cy <- CytoscapeConnection() | |
| cw <- new.CytoscapeWindow("demo", graph=makeSimpleGraph(), overwriteWindow=TRUE) | |
| displayGraph(cw) | |
| layoutNetwork(cw) |
cannin
/ installPackages.R
Last active
February 29, 2024 19:02
Install/update necessary packages from CRAN, Bioconductor, GitHub, or local source given a vector of strings with names of packages or DCF-based parameter file
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| #' Install/update necessary packages from CRAN, Bioconductor, GitHub, or local sources | |
| #' | |
| #' @param file a file with packages; overrides packages parameter | |
| #' @param packages a vector of strings with names of packages from CRAN, Bioconductor, GitHub | |
| #' @param updatePackages whether to update existing packages (Default: FALSE) | |
| #' @param dryRun whether to test for missing packages (Default: FALSE) | |
| #' | |
| #' @example | |
| #' \dontrun { | |
| #' source("https://gist.githubusercontent.com/cannin/6b8c68e7db19c4902459/raw/installPackages.R") |
cannin
/ convertVectorCallToString.R
Last active
August 29, 2015 14:03
Convert R vector into a call object and then convert the "call" object to a character string; this was useful for converting a vector back into code when generating knitr reports using brew
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| # Convert R vector into a call object and then convert the "call" object to a character string | |
| # This was useful for converting a vector back into code when generating knitr reports using brew | |
| tmp <- c("A", "B", "C") | |
| deparse(do.call(call, as.list(c("c", tmp)))) | |
| # [1] "c(\"A\", \"B\", \"C\")" |
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| #' Extract calls to functions | |
| #' | |
| #' Extracts function and file names for functions from a set of files | |
| #' | |
| #' @param path a directory path to files to be examined | |
| #' @param regexp a regular expression to find function calls | |
| #' @param fileRegexp a regular expression for files to be examined (e.g. '.R$') | |
| #' @param verbose a boolean whether to print debugging information | |
| #' | |
| #' @return a data.frame with two columns: 'function', the name of the function and |
cannin
/ jenkins_build.R
Last active
September 18, 2016 19:32
Generate testthat TAP results compatible with the Jenkins continuous integration TAP plugin
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| setRepositories(ind=1:6) | |
| options(repos="http://cran.rstudio.com/") | |
| if(!require(devtools)) install.packages("devtools") | |
| if(!require(testthat)) install.packages("testthat") | |
| if(Sys.getenv("TEST_DIR") != "") { | |
| testDir <- Sys.getenv("TEST_DIR") | |
| } else { | |
| testDir <- "inst/tests" |
cannin
/ deployAppWithData.R
Last active
August 29, 2015 14:11
Deploys a R Shiny app, but first copies the RData from the data folder
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| if (!require("devtools")) install.packages("devtools") | |
| library(devtools) | |
| if (!require("shinyapps")) devtools::install_github("rstudio/shinyapps") | |
| library(shinyapps) | |
| # Set working directory to root directory of package | |
| #setwd(TOP_LEVEL_PACKAGE_DIRECTORY) | |
| # Copy data from data folder |
cannin
/ jenkins_build_install.R
Last active
January 6, 2017 18:44
Generate testthat TAP results compatible with the Jenkins continuous integration TAP plugin
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| # PARAMETERS | |
| #cfg <- '{"url":"https://devbotcc:devbotcc@bitbucket.org/mil2041/netboxr.git", "quick":true, "dependencies":true}' | |
| #pkg <- "netboxr" | |
| #url <- Sys.getenv("URL") | |
| pkg <- Sys.getenv("PKG") | |
| cfg <- Sys.getenv("CFG") | |
| # FUNCTIONS | |
| processTap <- function(inputFile) { |
cannin
/ installPkgFromDir.R
Created
May 28, 2015 20:49
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| library(devtools) | |
| install(".") |
cannin
/ basicTraversal_3.groovy
Last active
May 10, 2021 12:53
BioPAX Tutorial; Examples from the Paxtools User's Guide. (PubMed ID: 24068901 Link: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003194)
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| //BASIC TRAVERSAL | |
| // Get names for all elements in a BioPAX OWL file and then for just Proteins | |
| import org.biopax.paxtools.io.BioPAXIOHandler; | |
| import org.biopax.paxtools.io.SimpleIOHandler; | |
| import org.biopax.paxtools.model.Model; | |
| import org.biopax.paxtools.model.BioPAXElement; | |
| import org.biopax.paxtools.model.level3.Protein; | |
| // Load a sample test BioPAX File via Simple IO Handler | |
| InputStream f = new FileInputStream(new File("data/biopax3-short-metabolic-pathway.owl")); |
cannin
/ pcviz.properties
Last active
September 3, 2015 12:49
— forked from armish/pcviz.properties
pcviz.properties
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| # Pathway commons | |
| pathwaycommons.url=http://www.pathwaycommons.org/pc2/ | |
| # BioGene | |
| biogene.url=http://cbio.mskcc.org/biogene/ | |
| biogene.format=json | |
| # iHop | |
| ihop.url=http://www.ihop-net.org/UniPub/iHOP/ |
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