diff --git a/.Rbuildignore b/.Rbuildignore index 0e7b5e5..bde0bac 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -57,3 +57,4 @@ import_pathcommons.R paxtoolsr.R plots_directed.html ^Meta$ +^CRAN-SUBMISSION$ diff --git a/DESCRIPTION b/DESCRIPTION index 0ea738f..385ec56 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: graphsim Type: Package Title: Simulate Expression Data from 'igraph' Networks -Version: 1.0.2 -Date: 2021-07-27 +Version: 1.0.3 +Date: 2022-09-10 Authors@R: c(person("S. Thomas", "Kelly",email = "tomkellygenetics@gmail.com", role = c("aut", "cre")), person("Michael A.", "Black", email = "mik.black@otago.ac.nz", role = c("aut", "ths")), person("Robrecht", "Cannoodt", role = c("ctb")), @@ -12,7 +12,7 @@ License: GPL-3 URL: https://github.com/TomKellyGenetics/graphsim/ BugReports: https://github.com/TomKellyGenetics/graphsim/issues/ Depends: R (>= 2.10) -Imports: utils, gplots, igraph, mvtnorm, Matrix, matrixcalc, graphics +Imports: gplots, igraph, mvtnorm, matrixcalc, Matrix, graphics Suggests: devtools, knitr (>= 1.5), markdown, prettydoc, R.rsp, rmarkdown, testthat, scales, vdiffr LazyData: TRUE diff --git a/NAMESPACE b/NAMESPACE index d8866d8..f1c9699 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -21,8 +21,6 @@ export(make_state_matrix) export(plot_directed) import(graphics) import(igraph) -importClassesFrom(Matrix,dgCMatrix) -importFrom(Matrix,Matrix) importFrom(Matrix,nearPD) importFrom(gplots,heatmap.2) importFrom(igraph,E) diff --git a/NEWS.md b/NEWS.md index d30670f..12439b0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,13 @@ +# graphsim 1.0.3 + +Minor update to pass CRAN checks + +- removed imports for unused packages + +- removed dependency on deprecated sparse matrices + +- correct links in citations and vignettes + # graphsim 1.0.2 Updates maintainer contact details. diff --git a/R/graphsim-package.R b/R/graphsim-package.R index 1675cde..4a8d069 100644 --- a/R/graphsim-package.R +++ b/R/graphsim-package.R @@ -522,7 +522,7 @@ #' } #' #' This plotting function is demonstrated in more detail -#' in the \href{https://CRAN.R-project.org/package=graphsim/vignettes/plots_directed.html}{plotting} vignette. +#' in the plots_directed.Rmd plotting vignette. #' #' @section Further information: #' The graphsim package is published in the \emph{Journal of Open Source Software}. diff --git a/R/laplacian.R b/R/laplacian.R index 524c1a8..b478049 100644 --- a/R/laplacian.R +++ b/R/laplacian.R @@ -13,8 +13,6 @@ ##' @keywords graph network igraph Laplacian ##' @importFrom igraph laplacian_matrix graph.edgelist as.undirected graph_from_adjacency_matrix ##' @import igraph -##' @importFrom Matrix Matrix -##' @importClassesFrom Matrix dgCMatrix ##' ##' @family graphsim functions ##' @family graph conversion functions diff --git a/README.md b/README.md index 019cc87..08289b8 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -[![Travis-CI Build Status](https://travis-ci.com/TomKellyGenetics/graphsim.svg?branch=master)](https://travis-ci.com/TomKellyGenetics/graphsim) -[![CircleCI build status](https://circleci.com/gh/TomKellyGenetics/graphsim.svg?style=svg)](https://circleci.com/gh/TomKellyGenetics/graphsim) +[![Travis-CI Build Status](https://www.travis-ci.com/TomKellyGenetics/graphsim.svg?branch=master)](https://app.travis-ci.com/github/mikblacklab/graphsim) +[![CircleCI build status](https://app.circleci.com/pipelines/github/TomKellyGenetics/graphsim.svg?style=svg)](https://app.circleci.com/pipelines/github/TomKellyGenetics/graphsim) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/TomKellyGenetics/graphsim?branch=master&svg=true)](https://ci.appveyor.com/project/TomKellyGenetics/graphsim) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) @@ -16,7 +16,7 @@ # graphsim -## Version 1.0.2 +## Version 1.0.3 ### Simulate Expression Data from 'igraph' Networks @@ -109,7 +109,7 @@ This will display a help page and link to documentation for each function. To cite package 'graphsim' in publications use: >S. Thomas Kelly and Michael A. Black (2020). graphsim: Simulate Expression Data from ->'igraph' Networks. R package version 1.0.2. +>'igraph' Networks. R package version 1.0.3. >https://github.com/TomKellyGenetics/graphsim doi:10.5281/zenodo.3931288 A BibTeX entry for LaTeX users is: @@ -119,7 +119,7 @@ A BibTeX entry for LaTeX users is: title = {{graphsim}: Simulate Expression Data from 'igraph' Networks }, author = {S. Thomas Kelly and Michael A. Black}, year = {2020}, - note = {R package version R package version 1.0.2.}, + note = {R package version R package version 1.0.3.}, url = {https://github.com/TomKellyGenetics/graphsim}, doi = {10.5281/zenodo.3931288}, } diff --git a/cran-comments.md b/cran-comments.md index 0a36865..3b50a52 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -7,12 +7,12 @@ * Fedora (devel) Linux, R-devel, clang, gfortran * MacOS 8.6.0 R R 3.6.2 * MacOS Mojave 10.14.6 R 3.6.1, R 3.6.2, R 4.0.2 -* MacOS Catalina 10.15.5 R 4.0.2 +* MacOS Catalina 10.15.7 R 4.2.0 ## Local R CMD check results -── R CMD check results ───────────────────────────────────── graphsim 1.0.2 ──── -Duration: 57.9s +── R CMD check results ───────────────────────────────────── graphsim 1.0.3 ──── +Duration: 1m 55.4s 0 errors ✓ | 0 warnings ✓ | 0 notes ✓ diff --git a/inst/CITATION b/inst/CITATION index 877d6af..99bf282 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -4,7 +4,7 @@ citHeader("To cite package 'graphsim' in publications use:") desc <- packageDescription("graphsim") if(is.na(desc[1])){ year <- "2020" - vers <- "1.0.2" + vers <- "1.0.3" } else { year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", desc$Date) vers <- paste("R package version", desc$Version) diff --git a/man/graphsim-package.Rd b/man/graphsim-package.Rd index cf81089..78df43b 100644 --- a/man/graphsim-package.Rd +++ b/man/graphsim-package.Rd @@ -520,7 +520,7 @@ plot_directed(graph_pathway, } This plotting function is demonstrated in more detail -in the \href{https://CRAN.R-project.org/package=graphsim/vignettes/plots_directed.html}{plotting} vignette. +in the plots_directed.Rmd plotting vignette. } \section{Further information}{ diff --git a/vignettes/simulate_expression.Rmd b/vignettes/simulate_expression.Rmd index 181b6ba..73cbdb1 100644 --- a/vignettes/simulate_expression.Rmd +++ b/vignettes/simulate_expression.Rmd @@ -49,7 +49,7 @@ If you have problems or feedback, sumbmitting an issue to the the GitHub reposit Pathway and graph structures have a wide array of applications. Here we consider the simulation of (log-normalised) gene expression data from a biological pathway. If you have another use for this software you are welcome to apply it to your problem but please bear in mind that it was designed with this application in mind. In principle, normally-distributed continuous data can be generated based on any defined relationships. This package uses the graph structure to define a ∑ covariance matrix and generate simulated data by sampling from a multivariate normal distribution. -Crucially, this allows the simulation of negative correlations based on inhibitory or repressive relationships, as commonly occur in biology (Barabási and Oltvai 2004). A custom plotting function `plot_directed` is provided to visualise these relationships using the "state" parameter. This plotting function has a [dedicated vignette](https://CRAN.R-project.org/package=graphsim/vignettes/plots_directed.html). +Crucially, this allows the simulation of negative correlations based on inhibitory or repressive relationships, as commonly occur in biology (Barabási and Oltvai 2004). A custom plotting function `plot_directed` is provided to visualise these relationships using the "state" parameter. This plotting function has a dedicated vignette: plots_directed.Rmd. For more details on the background of this package, see the [paper](https://github.com/TomKellyGenetics/graphsim/blob/master/paper/paper.Rmd) included with the package on GitHub. This vignette provides more detail on the code needed to reproduce the figures presented in the manuscript. diff --git a/vignettes/simulate_expression.html b/vignettes/simulate_expression.html index 35dbe9c..274a076 100644 --- a/vignettes/simulate_expression.html +++ b/vignettes/simulate_expression.html @@ -227,7 +227,7 @@

1 Overview of graphsim

1.1 Motivations

Pathway and graph structures have a wide array of applications. Here we consider the simulation of (log-normalised) gene expression data from a biological pathway. If you have another use for this software you are welcome to apply it to your problem but please bear in mind that it was designed with this application in mind. In principle, normally-distributed continuous data can be generated based on any defined relationships. This package uses the graph structure to define a ∑ covariance matrix and generate simulated data by sampling from a multivariate normal distribution.

-

Crucially, this allows the simulation of negative correlations based on inhibitory or repressive relationships, as commonly occur in biology (Barabási and Oltvai 2004). A custom plotting function plot_directed is provided to visualise these relationships using the “state” parameter. This plotting function has a dedicated vignette.

+

Crucially, this allows the simulation of negative correlations based on inhibitory or repressive relationships, as commonly occur in biology (Barabási and Oltvai 2004). A custom plotting function plot_directed is provided to visualise these relationships using the “state” parameter. This plotting function has a dedicated vignette: plots_directed.Rmd..

For more details on the background of this package, see the paper included with the package on GitHub. This vignette provides more detail on the code needed to reproduce the figures presented in the manuscript.