--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GSVA.R	Thu May 20 08:30:22 2021 +0000
@@ -0,0 +1,75 @@
+###############################################################################
+# title: Gene set variation analysis
+# author: Xiaowei
+# time: Mar.31 2021
+###############################################################################
+#=================================================================
+#how to pass parameters
+#=================================================================
+spec <- matrix(c("expr", 'E', 1, 'character', 'Gene expression data which is an CSV file of expression values where rows correspond to genes and columns correspond to samples.',
+                 "geneSet", 'G', 1, 'character', 'Gene set',
+                 'gene_Identifier_class','C', 1, 'character', 'Gene Identifier class of GeneSet',
+                 'method', "M", 1,'character', 'One of gsva, ssgsea, zscore, plage',
+                 'img_file', 'I', 1,'character', 'img_file',
+                 'img_type', 'T', 1,'character', 'PDF, PNG, JPEG',
+                 'img_width', 'W', 1, 'integer', 'the img file width',
+                 'img_height', 'H', 1, 'integer', 'the img file height',
+                 'GSVA_result', 'R', 1, 'character', 'Result of GSVA, an CSV file.'
+                 
+                 ),
+               byrow = TRUE, ncol = 5)
+
+
+if (!requireNamespace("getopt", quietly = TRUE))
+  install.packages("getopt")
+
+opt <- getopt::getopt(spec)
+
+#----------------
+#整理参数
+#----------------
+
+if(is.null(opt$gene_Identifier_class)){gene_Identifier_class = 'Symbol'}else{gene_Identifier_class = opt$gene_Identifier_class }
+if(is.null(opt$method)){opt$method = 'gsva'}
+if(is.null(opt$img_type)){opt$img_type = 'PNG'}
+if(is.null(opt$img_width)){img_width = 900}else{img_width = opt$img_width}
+if(is.null(opt$img_height)){img_height = 900}else{img_height = opt$img_height}
+
+#================================================================
+#run codes
+#================================================================
+gsva_input_data <- read.csv(opt$expr, row.names = 1)
+
+# if (gene_Identifier_class == 'Symbol'){
+#   geneset <- GSEABase::getGmt(opt$geneSet, 
+#                               geneIdType = GSEABase::SymbolIdentifier())
+# }else{
+#   geneset <- GSEABase::getGmt(opt$geneSet, 
+#                               geneIdType = GSEABase::EntrezIdentifier())
+# }
+
+load(opt$geneSet)
+
+result <- GSVA::gsva(as.matrix(gsva_input_data), geneSet, mx.diff=FALSE, 
+               verbose=FALSE, parallel.sz=2, method = opt$method)
+#================================================================
+#output
+#================================================================
+
+write.csv(result, file = opt$GSVA_result)
+
+if (opt$img_type == 'PNG'){
+  png(filename = opt$img_file, width = img_width, height = img_height)
+}else if(opt$img_type == 'JPG'){
+  jpeg(filename = opt$img_file, width = img_width, height = img_height)
+}else{
+  pdf(file = opt$img_file, width = img_width, height = img_height)
+}
+
+pheatmap::pheatmap(result, scale = "row", main = "heatmap", show_colnames=T)
+dev.off()
+
+
+
+
+