Merge branch 'release/v1.0.0' into main

DESCRIPTION

@@ -1,19 +1,19 @@
-Package: dbfmcl
+Package: scigenex
 Type: Package
-Title: The DBFMCL algorithm
-Version: 0.1.8
+Title: The scigenex package (Single-Cell Informative GENe Explorer)
+Version: 1.0.0
 Date: 2020-07-22
-Author: Aurelie Bergon, J. Bavais, Fabrice Lopez, Julien Textoris, Samuel Granjeaud, Lionel Spinelli and Denis Puthier
-Maintainer: D. Puthier <denis.puthier@univ-amu.fr>
+Author: J. Bavais, Aurelie Bergon, Fabrice Lopez, Julien Textoris, Samuel Granjeaud, Lionel Spinelli and Denis Puthier
+Maintainer: J. Bavais <julie.bavais@yahoo.fr>
 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, 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
 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

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"

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)
@@ -31,6 +28,6 @@ export(DBFMCL,
         plot_clust,
         load_seurat,
         write_clust,
-        VERBOSITY_DBFMCL)
+        VERBOSITY_SCIGENEX)
 
 

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
 #########################################################

R/zzz.R

@@ -1,3 +1,3 @@
 # .First.lib <- function(lib,pkg) {
-#    library.dynam("dbfmcl",pkg,lib)
+#    library.dynam("scigenex",pkg,lib)
 # }

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/).
+Documentation (in progress) is available at [https://dputhier.github.io/scigenex/](https://dputhier.github.io/scigenex/).