1. CoGAPS
  2. Commit 080fd044ecbfdbe427bd890f4baa87a8f91bfe1c
Browse code

passing checks

Tom Sherman authored on 05/06/2018 22:04:02
Showing 24 changed files
.Rbuildignore
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@@ -9,17 +9,27 @@
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 ^inst/profiling/
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 ^inst/vignettes/
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-^src/Algorithms.o
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-^src/AtomicSupport.o
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+^src/AtomicDomain.o
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 ^src/Cogaps.o
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+^src/GapsRunner.o
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+^src/GapsStatistics.o
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 ^src/GibbsSampler.o
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-^src/Matrix.o
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-^src/Random.o
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+^src/ProposalQueue.o
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 ^src/RcppExports.o
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 ^src/test-runner.o
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+^src/data_structures/Matrix.o
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+^src/data_structures/Vector.o
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+^src/file_parser/CsvParser.o
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+^src/file_parser/TsvParser.o
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+^src/file_parser/MtxParser.o
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+^src/math/Algorithms.o
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+^src/math/Random.o
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 ^src/cpp_tests/testAlgorithms.o
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-^src/cpp_tests/testAtomicSupport.o
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+^src/cpp_tests/testAtomicDomain.o
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+^src/cpp_tests/testEfficientSets.o
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+^src/cpp_tests/testFileParsers.o
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+^src/cpp_tests/testGapsRunner.o
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 ^src/cpp_tests/testGibbsSampler.o
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 ^src/cpp_tests/testMatrix.o
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-^src/cpp_tests/testRandom.o
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-^src/cpp_tests/testSerialization.o
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\ No newline at end of file
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+^src/cpp_tests/testProposalQueue.o
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+^src/cpp_tests/testRandom.o
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DESCRIPTION
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@@ -14,7 +14,7 @@ Description: Coordinated Gene Activity in Pattern Sets (CoGAPS)
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 Maintainer: Elana J. Fertig <ejfertig@jhmi.edu>,
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     Thomas D. Sherman <tomsherman159@gmail.com>
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 Depends:
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-    R (>= 3.3.0),
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+    R (>= 3.4.0),
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     Rcpp (>= 0.11.0)
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 Imports:
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     RColorBrewer (>= 1.0.5),
R/CoGAPS.R
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@@ -34,6 +34,7 @@
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 #' @param fixedPatterns matrix of fixed values in either A or P matrix
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 #' @param checkpointInterval time (in seconds) between creating a checkpoint
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 #' @param checkpointFile name of the checkpoint file
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+#' @param nCores number of cpu cores to run in parallel over
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 #' @param ... keeps backwards compatibility with arguments from older versions
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 #' @return list with A and P matrix estimates
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 #' @importFrom methods new
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@@ -130,6 +131,12 @@ CoGapsFromCheckpoint <- function(D, S, path, checkpointFile=NA)
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 #' CoGAPS with file input for matrix
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 #' @export
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+#'
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+#' @param D file path for data matrix
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+#' @return list with A and P matrix estimates
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+#' @examples
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+#'  file <- system.file("extdata/GIST.mtx", package="CoGAPS")
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+#'  CoGAPSFromFile(file)
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 CoGAPSFromFile <- function(D)
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 {
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     cogapsFromFile_cpp(D)
R/package.R
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@@ -38,3 +38,69 @@
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 #' @import ggplot2
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 #' @useDynLib CoGAPS
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 NULL
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+
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+#' Simulated data
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+#' @docType data
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+#' @name SimpSim.D
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+#' @usage SimpSim.D
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+NULL
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+
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+#' Simulated data
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+#' @docType data
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+#' @name SimpSim.S
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+#' @usage SimpSim.S
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+NULL
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+
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+#' Simulated data
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+#' @docType data
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+#' @name SimpSim.A
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+#' @usage SimpSim.A
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+NULL
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+
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+#' Simulated data
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+#' @docType data
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+#' @name SimpSim.P
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+#' @usage SimpSim.P
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+NULL
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+
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+#' CoGAPS result from running on simulated data
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+#' @docType data
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+#' @name SimpSim.result
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+#' @usage SimpSim.result
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+NULL
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+
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+#' Sample GIST gene expression data from Ochs et al. (2009)
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+#' @docType data
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+#' @name GIST.D
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+#' @usage GIST.D
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+NULL
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+
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+#' Sample GIST gene expression data from Ochs et al. (2009)
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+#' @docType data
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+#' @name GIST.S
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+#' @usage GIST.S
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+NULL
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+
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+#' Simulated dataset to quantify gene set membership in the GIST dataset
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+#' @docType data
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+#' @name GIST.GeneSets
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+#' @usage GIST.GeneSets
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+NULL
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+
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+#' CoGAPS result from running on GIST dataset
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+#' @docType data
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+#' @name GIST.result
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+#' @usage GIST.result
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+NULL
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+
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+#' Simulated dataset to quantify gene set membership.
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+#' @docType data
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+#' @name GSets
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+#' @usage GSets
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+NULL
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+
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+#' Gene sets defined by transcription factors defined from TRANSFAC.
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+#' @docType data
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+#' @name tf2ugFC
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+#' @usage tf2ugFC
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+NULL
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\ No newline at end of file
R/plotGAPS.R
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@@ -11,22 +11,39 @@
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 #' data(SimpSim)
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 #' plotGAPS(SimpSim.result$Amean, SimpSim.result$Pmean)
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 #' @export
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-plotGAPS <- function(A, P, filename=NULL)
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+plotGAPS <- function(A, P, outputPDF="")
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 {
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-    if (!is.null(pdf))
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+    if (outputPDF != "")
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     {
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-        pdf(file=paste(filename, "-Patterns", ".pdf", sep=""))
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+        pdf(file=paste(outputPDF, "-Patterns", ".pdf", sep=""))
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+    }
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+    else
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+    {
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+        dev.new()
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     }
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-    plotP(P)
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-    if (!is.null(pdf))
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+    arrayIdx <- 1:ncol(P)
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+    maxP <- max(P)
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+    nPatt <- dim(P)[1]
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+    matplot(arrayIdx, t(P), type='l', lwd=3, xlim=c(1,ncol(P)), ylim=c(0,maxP),
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+        xlab='Samples',ylab='Relative Strength',col=rainbow(nPatt))
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+    title(main='Inferred Patterns')
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+    legend("topright", paste("Pattern", 1:nPatt, sep = ""), pch = 1:nPatt,
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+        lty=1,cex=0.8,col=rainbow(nPatt),bty="y",ncol=5)
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+
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+    if (outputPDF == "")
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     {
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-        pdf(file=paste(filename, "-Amplitude", ".pdf", sep=""))
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+        dev.new()
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+    }
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+    else
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+    {
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+        dev.off()
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+        pdf(file=paste(outputPDF, "-Amplitude", ".pdf", sep=""))
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     }
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-    heatmap(A, Rowv=NA, Colv=NA)
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-    if (!is.null(pdf))
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+    heatmap(A, Rowv=NA, Colv=NA)
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+    if (outputPDF != "")
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     {
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         dev.off()
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     }
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-}
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+}
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\ No newline at end of file
data/GIST.csv
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similarity index 100%
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rename from data/GIST.csv
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rename to inst/extdata/GIST.csv
data/GIST.mtx
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similarity index 100%
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rename from data/GIST.mtx
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rename to inst/extdata/GIST.mtx
data/GIST.tsv
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similarity index 100%
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rename from data/GIST.tsv
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rename to inst/extdata/GIST.tsv
man/CoGAPS.Rd
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@@ -51,6 +51,8 @@ the fixed patterns}
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 \item{checkpointFile}{name of the checkpoint file}
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+\item{nCores}{number of cpu cores to run in parallel over}
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+
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 \item{...}{keeps backwards compatibility with arguments from older versions}
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 }
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 \value{
man/CoGAPSFromFile.Rd
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@@ -6,7 +6,17 @@
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 \usage{
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 CoGAPSFromFile(D)
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 }
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+\arguments{
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+\item{D}{file path for data matrix}
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+}
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+\value{
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+list with A and P matrix estimates
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+}
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 \description{
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 CoGAPS with file input for matrix
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 }
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+\examples{
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+ file <- system.file("extdata/GIST.mtx", package="CoGAPS")
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+ CoGAPSFromFile(file)
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+}
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man/GIST.D.Rd
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new file mode 100644
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@@ -0,0 +1,13 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{GIST.D}
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+\alias{GIST.D}
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+\title{Sample GIST gene expression data from Ochs et al. (2009)}
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+\usage{
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+GIST.D
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+}
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+\description{
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+Sample GIST gene expression data from Ochs et al. (2009)
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+}
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+
man/GIST.GeneSets.Rd
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new file mode 100644
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{GIST.GeneSets}
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+\alias{GIST.GeneSets}
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+\title{Simulated dataset to quantify gene set membership in the GIST dataset}
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+\usage{
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+GIST.GeneSets
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+}
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+\description{
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+Simulated dataset to quantify gene set membership in the GIST dataset
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+}
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+
man/GIST.S.Rd
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new file mode 100644
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{GIST.S}
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+\alias{GIST.S}
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+\title{Sample GIST gene expression data from Ochs et al. (2009)}
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+\usage{
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+GIST.S
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+}
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+\description{
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+Sample GIST gene expression data from Ochs et al. (2009)
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+}
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+
man/GIST.result.Rd
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new file mode 100644
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{GIST.result}
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+\alias{GIST.result}
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+\title{CoGAPS result from running on GIST dataset}
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+\usage{
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+GIST.result
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+}
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+\description{
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+CoGAPS result from running on GIST dataset
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+}
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+
man/GSets.Rd
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new file mode 100644
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{GSets}
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+\alias{GSets}
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+\title{Simulated dataset to quantify gene set membership.}
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+\usage{
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+GSets
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+}
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+\description{
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+Simulated dataset to quantify gene set membership.
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+}
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+
man/SimpSim.A.Rd
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@@ -0,0 +1,13 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{SimpSim.A}
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+\alias{SimpSim.A}
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+\title{Simulated data}
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+\usage{
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+SimpSim.A
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+}
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+\description{
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+Simulated data
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+}
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+
man/SimpSim.D.Rd
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{SimpSim.D}
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+\alias{SimpSim.D}
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+\title{Simulated data}
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+\usage{
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+SimpSim.D
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+}
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+\description{
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+Simulated data
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+}
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+
man/SimpSim.P.Rd
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new file mode 100644
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{SimpSim.P}
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+\alias{SimpSim.P}
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+\title{Simulated data}
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+\usage{
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+SimpSim.P
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+}
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+\description{
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+Simulated data
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+}
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+
man/SimpSim.S.Rd
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@@ -0,0 +1,13 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{SimpSim.S}
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+\alias{SimpSim.S}
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+\title{Simulated data}
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+\usage{
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+SimpSim.S
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+}
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+\description{
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+Simulated data
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+}
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+
man/SimpSim.result.Rd
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new file mode 100644
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{SimpSim.result}
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+\alias{SimpSim.result}
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+\title{CoGAPS result from running on simulated data}
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+\usage{
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+SimpSim.result
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+}
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+\description{
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+CoGAPS result from running on simulated data
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+}
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+
man/plotGAPS.Rd
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@@ -4,7 +4,7 @@
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 \alias{plotGAPS}
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 \title{Plot Decomposed A and P Matrices}
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 \usage{
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-plotGAPS(A, P, filename = NULL)
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+plotGAPS(A, P, outputPDF = "")
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 }
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 \arguments{
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 \item{A}{the mean A matrix}
man/tf2ugFC.Rd
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/package.R
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+\docType{data}
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+\name{tf2ugFC}
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+\alias{tf2ugFC}
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+\title{Gene sets defined by transcription factors defined from TRANSFAC.}
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+\usage{
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+tf2ugFC
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+}
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+\description{
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+Gene sets defined by transcription factors defined from TRANSFAC.
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+}
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+
src/cpp_tests/testFileParsers.cpp
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@@ -26,7 +26,7 @@ TEST_CASE("Test Parsers")
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         std::string line(mtxPath);
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         //std::getline(is, line);
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-        std::cout << "\n" <<  line << "\nTHIS IS TEST OUTPUT\n";
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+        Rcpp::Rcout << "\n" <<  line << "\nTHIS IS TEST OUTPUT\n";
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         //is.close();
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     }
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 }
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\ No newline at end of file
vignettes/CoGAPSUsersManual.Rnw
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@@ -356,4 +356,4 @@ for (tf in TFs) {
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 \bibliographystyle{plain}
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 \bibliography{AppNote}
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-\end{document}
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+\end{document}
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