From 8d09e6a5377b3eac199ce20823a3bae97ff516f5 Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 27 Aug 2021 10:13:50 +0200 Subject: [PATCH 1/4] Changed to scige --- R/dbfmcl_main.R | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/R/dbfmcl_main.R b/R/dbfmcl_main.R index eaf3363..1223dc0 100644 --- a/R/dbfmcl_main.R +++ b/R/dbfmcl_main.R @@ -1,7 +1,7 @@ ################################################################ -## Main script of the R PACKAGE : DBFMCL +## Main script of the R PACKAGE : scigenex ## -## Authors : BERGON A, J. BAVAIS +## Authors : J. BAVAIS, BERGON A, ## with the collaboration of LOPEZ F., TEXTORIS J. and PUTHIER D. ## ## @@ -13,14 +13,14 @@ # 1 : info # 2 : DEBUG -VERBOSITY_DBFMCL = 3 +VERBOSITY_SCIGENEX = 3 print_msg <- function(msg, msg_type="INFO"){ if(msg_type == "INFO") - if(VERBOSITY_DBFMCL > 0) + if(VERBOSITY_SCIGENEX > 0) cat(paste("|-- ", msg, "\n")) if(msg_type == "DEBUG") - if(VERBOSITY_DBFMCL > 1) + if(VERBOSITY_SCIGENEX > 1) cat(paste("|-- ", msg, "\n")) if(msg_type == "WARNING") cat(paste("|-- ", msg, "\n")) @@ -252,7 +252,7 @@ setMethod( #' @title #' load_seurat #' @description -#' Load a seurat object into a DBFMCL. At the moment the objective is mainly +#' Load a seurat object into a ClusterSet object. At the moment the objective is mainly #' to store cell identity (i.e cell types/groups to barcode mapping) and #' cell type to color mapping. #' @param object A ClusterSet object. @@ -284,7 +284,7 @@ setMethod("load_seurat", stop("Please provide a Seurat and patchwork object.") } if(ncol(object) != ncol(seurat_obj)){ - stop("The number of cells is not the same in DBFMCL and Seurat Object.") + stop("The number of cells is not the same in ClusterSet object and Seurat object.") } g <- ggplot2::ggplot_build(dimplot_obj) @@ -774,9 +774,14 @@ setMethod( #' \code{mcl -h} #' @author Bergon A., Bavais J., Textoris J., Granjeaud S., Lopez F and Puthier #' D. -#' @references Van Dongen S. (2000) A cluster algorithm for graphs. National +#' @references +#' - Van Dongen S. (2000) A cluster algorithm for graphs. National #' Research Institute for Mathematics and Computer Science in the 1386-3681. -#' @keywords manip +#' - Lopez F.,Textoris J., Bergon A., Didier G., Remy E., Granjeaud +#' S., Imbert J. , Nguyen C. and Puthier D. TranscriptomeBrowser: a powerful +#' and flexible toolbox to explore productively the transcriptional landscape +#' of the Gene Expression Omnibus database. PLoSONE, 2008;3(12):e4001. +#' @keywords clustering, gene expression, classification, MCL. #' @examples #' #' \dontrun{ @@ -1302,5 +1307,5 @@ get_data_4_DBFMCL <- function(data = NULL, filename = NULL, path = ".") { return(list(data = data, name = name)) } ######################################################### -## END PACKAGE DBFMCL +## END PACKAGE scigenex ######################################################### From 475bf6b7a9207dc110af29568050794373d573a9 Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 27 Aug 2021 10:35:05 +0200 Subject: [PATCH 2/4] Changed to scigenex --- DESCRIPTION | 14 +++++++------- Makefile | 6 +++--- NAMESPACE | 2 +- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 80e4c8d..8a7e9ed 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,19 +1,19 @@ -Package: dbfmcl +Package: scigenex Type: Package -Title: The DBFMCL algorithm +Title: The scigenex package (Single-Cell Informative GENe Explorer) Version: 0.1.8 Date: 2020-07-22 -Author: Aurelie Bergon, J. Bavais, Fabrice Lopez, Julien Textoris, Samuel Granjeaud, Lionel Spinelli and Denis Puthier -Maintainer: D. Puthier +Author: J. Bavais, Aurelie Bergon, Fabrice Lopez, Julien Textoris, Samuel Granjeaud, Lionel Spinelli and Denis Puthier +Maintainer: J. Bavais Depends: R (>= 3.6.1), methods, testthat Imports: reshape2, ggplot2, magrittr, dplyr, igraph, MCL Collate: dbfmcl_main.R zzz.R -Description: The dbfmcl package (Density Based Filtering And Markov Clustering) implement a method for filtering and partionning a noisy dataset. DBF-MCL is a tree-step adaptative algorithm that (i) find elements located in dense areas (ie. clusters) (ii) uses selected items to construct a graph and (iii) performs graph partitioning using MCL. -biocViews: Clustering, Classification +Description: The scigenex package (Single-Cell Informative GENe Explorer) proposes a set of functions to extract informative genes from a scRNA-seq experiment and search for clusters of co-expressed genes. These clusters are annotated and can be mapped onto UMAP or t-SNE diagram to functionally annotate cell populations. +biocViews: Clustering, Classification, Transcriptomics, SingleCell, ReportWriting, GeneRegulation License: GPL-3 Suggests: RColorBrewer LazyLoad: yes -URL: https://github.com/dputhier/dbfmcl +URL: https://github.com/dputhier/sigenex Packaged: 2009-10-28 09:39:36 UTC; biocbuild RoxygenNote: 7.1.1 Encoding: UTF-8 diff --git a/Makefile b/Makefile index 636d120..abe192d 100644 --- a/Makefile +++ b/Makefile @@ -16,12 +16,12 @@ help: @echo "" clean: - @rm -f src/*.o src/*.so; rm -f dbfmcl.Rcheck/dbfmcl/libs/dbfmcl.so; rm -rf ./dbfmcl.Rcheck + @rm -f src/*.o src/*.so; rm -f scigenex.Rcheck/dbfmcl/libs/dbfmcl.so; rm -rf ./dbfmcl.Rcheck @rm -rf /tmp/dbfmcl; check: clean - @mkdir -p /tmp/dbfmcl; cp -r ./* /tmp/dbfmcl - @R CMD check /tmp/dbfmcl + @mkdir -p /tmp/scigenex; cp -r ./* /tmp/scigenex + @R CMD check /tmp/scigenex doc: @echo ">>> Creating a package documentation" diff --git a/NAMESPACE b/NAMESPACE index b0c14d6..0e5be59 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -31,6 +31,6 @@ export(DBFMCL, plot_clust, load_seurat, write_clust, - VERBOSITY_DBFMCL) + VERBOSITY_SCIGENEX) From 79af84537d57d7f4889130ebb11ddead7964b8fb Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 27 Aug 2021 10:41:46 +0200 Subject: [PATCH 3/4] Changed to scigenex --- README.md | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 46c5567..357bcec 100644 --- a/README.md +++ b/README.md @@ -1,39 +1,40 @@ -# dbfmcl +# scigenex -WARNING: dbfmcl library is still in beta version. +WARNING: scigenex library is still in beta version. ## Installation ### In the terminal - R CMD INSTALL dbfmcl + R CMD INSTALL scigenex # In R - library(dbfmcl) + library(scigenex) ### From R -The dbfmcl library is currently not available in CRAN or Bioc. To install from github, use: +The scigenex library is currently not available in CRAN or Bioc. To install from github, use: library(devtools) - install_github("dputhier/dbfmcl") + install_github("dputhier/scigenex") To install from a tar in the terminal - tar xvfz dbfmcl.tar.gz + tar xvfz scigenex.tar.gz R CMD INSTALL dbfmcl Or using the R interpreter: library(devtools) install("/path/to/the/package") - library("dbfmcl") + library("scigenex") ## Example ### Quick example on artificial data + library(scigenex) m <- matrix(rnorm(80000), nc=20) m[1:100,1:10] <- m[1:100,1:10] + 4 m[101:200,11:20] <- m[101:200,11:20] + 3 @@ -46,7 +47,7 @@ Or using the R interpreter: fdr = 10) plot_clust(res, ceil = 10, floor = -10) write_clust(res, "ALL.sign.txt") - + ### Documentation -Documentation (in progress) is available at [https://dputhier.github.io/dbfmcl/](https://dputhier.github.io/dbfmcl/). \ No newline at end of file +Documentation (in progress) is available at [https://dputhier.github.io/scigenex/](https://dputhier.github.io/scigenex/). \ No newline at end of file From cb78bdb9939b16c42d94b668fe58e2c19741a011 Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 27 Aug 2021 11:02:43 +0200 Subject: [PATCH 4/4] Going scigenex --- DESCRIPTION | 4 ++-- NAMESPACE | 7 ++----- R/zzz.R | 2 +- 3 files changed, 5 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8a7e9ed..23ed0b3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,14 +1,14 @@ Package: scigenex Type: Package Title: The scigenex package (Single-Cell Informative GENe Explorer) -Version: 0.1.8 +Version: 1.0.0 Date: 2020-07-22 Author: J. Bavais, Aurelie Bergon, Fabrice Lopez, Julien Textoris, Samuel Granjeaud, Lionel Spinelli and Denis Puthier Maintainer: J. Bavais Depends: R (>= 3.6.1), methods, testthat Imports: reshape2, ggplot2, magrittr, dplyr, igraph, MCL Collate: dbfmcl_main.R zzz.R -Description: The scigenex package (Single-Cell Informative GENe Explorer) proposes a set of functions to extract informative genes from a scRNA-seq experiment and search for clusters of co-expressed genes. These clusters are annotated and can be mapped onto UMAP or t-SNE diagram to functionally annotate cell populations. +Description: The scigenex package (Single-Cell Informative GENe Explorer) proposes a set of functions to extract informative genes from a scRNA-seq experiment, search and store clusters of co-expressed genes. These clusters are annotated and can be mapped onto UMAP or t-SNE diagram to functionally annotate cell populations. biocViews: Clustering, Classification, Transcriptomics, SingleCell, ReportWriting, GeneRegulation License: GPL-3 Suggests: RColorBrewer diff --git a/NAMESPACE b/NAMESPACE index 0e5be59..ba842e0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,15 +1,12 @@ if(.Platform$OS.type == "windows"){ - useDynLib("dbfml.dll") + useDynLib("scigenex.dll") }else{ - useDynLib("dbfmcl") + useDynLib("scigenex") } importClassesFrom(methods, character, list, matrix, vector) - importMethodsFrom(methods, show) - - importFrom("grDevices", "colorRampPalette") importFrom("methods", "new", "slot", "slotNames") importFrom("stats", "sd", dist, hclust, heatmap, median, rnorm) diff --git a/R/zzz.R b/R/zzz.R index c77ae61..ca218cf 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -1,3 +1,3 @@ # .First.lib <- function(lib,pkg) { -# library.dynam("dbfmcl",pkg,lib) +# library.dynam("scigenex",pkg,lib) # }