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dputhier · Jan 8, 2024 · 31f2585 · 31f2585
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,7 +6,7 @@ Date: 2020-07-22
 Author: J. Bavais, Sebastien Nin, Lionel Spinelli and Denis Puthier
 Maintainer: J. Bavais <julie.bavais@yahoo.fr>
 Depends: R (>= 4.0.0), methods
-Imports: scales, reshape2, ggplot2, dplyr, igraph, plotly, qlcMatrix, clusterProfiler, org.Hs.eg.db, org.Mm.eg.db, amap, grDevices, stats, utils, magrittr, testthat, iheatmapr, AnnotationDbi, data.table, enrichplot, SeuratObject, pheatmap, Seurat, Matrix, SparseM, ggforce, ggstar, patchwork, biomaRt, ggh4x, xlsx, pracma, jinjar, cluster, clValid, DT
+Imports: scales, reshape2, ggplot2, dplyr, igraph, plotly, qlcMatrix, clusterProfiler, org.Hs.eg.db, org.Mm.eg.db, amap, grDevices, stats, utils, magrittr, testthat, iheatmapr, AnnotationDbi, data.table, enrichplot, SeuratObject, pheatmap, Seurat, Matrix, SparseM, ggforce, ggstar, patchwork, biomaRt, ggh4x, WriteXLS, pracma, jinjar, cluster, clValid, DT
 Collate: ClusterSet_class.R import_package.R enrichment_analysis.R top_genes.R visualization.R get_data_for_scigenex.R get_genes.R reorder_genes.R utils.R dataset_doc.R plot_profiles.R filter_gene_clusters.R gene_clustering.R select_genes.R Visium_hull.R compare_gene_sets.R cluster_stats.R convert.R plot_spatial.R top_by_go.R dist2border.R clusterset_report.R module_quality_scores.R zzz.R
 Description: The scigenex package (Single-Cell Informative GENe Explorer) proposes a set of functions to (i) extract informative genes from a scRNA-seq and Visium experiment, (ii) search clusters of co-expressed genes, (iii) store/manipulate these clusters, (v) and anotate these clusters. These clusters can be mapped onto UMAP or t-SNE diagrams to functionally annotate cell populations.
 biocViews: Clustering, Classification, Transcriptomics, SingleCell, ReportWriting, GeneRegulation

diff --git a/R/ClusterSet_class.R b/R/ClusterSet_class.R
@@ -649,40 +649,44 @@ setGeneric("cluster_set_to_xls",
 #' dir.create(tp_dir, showWarnings = FALSE)
 #' cluster_set_to_xls(pbmc3k_medium_clusters, file.path(tp_dir, "test.xls"))
 #' @export cluster_set_to_xls
-setMethod("cluster_set_to_xls",            
-          signature("ClusterSet"), 
+setMethod("cluster_set_to_xls",
+          signature("ClusterSet"),
           function(object,
                    file_path = NULL) {
-
             check_format_cluster_set(object)
             object <- reorder_genes(object)
             dir_n <- dirname(file_path)
 
-            if(!dir.exists(dir_n))
+            if (!dir.exists(dir_n))
               print_msg("Directory does not exist. Exiting.", msg_type = "STOP")
 
 
-            if(file.exists(file_path))
+            if (file.exists(file_path))
               print_msg("File  already exist. Exiting.", msg_type = "STOP")
 
-
-              gnc <- gene_cluster(object)
-              xlsx::write.xlsx(data.frame(cluster=unname(gnc), "official_gene_symbol"=names(gnc)), 
-                               file=file_path, 
-                               sheetName="All_modules")
-
-
-              for(i in 1:nclust(object)){
-                xlsx::write.xlsx(data.frame("official_gene_symbol"=object@gene_clusters[[i]]), 
-                                 file=file_path, 
-                                 sheetName=paste0("Module ", i),
-                                 append =TRUE)
+
+            gnc <- gene_cluster(object)
+            df_list <- list(x=data.frame(All_modules = unname(gnc),
+                                         "official_gene_symbol" = names(gnc)))
+
+            tmp <- lapply(object@gene_clusters, as.data.frame)
+            for(i in 1:length(tmp)){
+              colnames(tmp[[i]]) <- paste0("Module ", i)
 
             }
+
+            df_list <- append(df_list, tmp)                           
+
+            WriteXLS::WriteXLS(
+              x=df_list,
+              ExcelFileName = file_path,
+              SheetNames = c("All_modules", paste0("Module ", 1:length(object@gene_clusters)))
+            )
+
+
 })
 
 
-
 ################################################################################
 ##      Method for reordering clusters from a clusterSet 
 ################################################################################