--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GSAR.R	Thu May 20 08:22:56 2021 +0000
@@ -0,0 +1,117 @@
+###############################################################################
+# title: Gene set analysis in R
+# author: Xiaowei
+# time: Mar.31 2021
+###############################################################################
+#=================================================================
+#how to pass parameters
+#=================================================================
+spec <- matrix(c("expr_file",'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_file", 'G', 1, 'character', 'Gene set',
+                 "design_file", 'D', 1, 'character', 'Design for the samples of expression data',
+                 "min_size", 'I',1, 'numeric','a numeric value indicating the minimum allowed gene set size. Default value is 10.',
+                 "max_size", 'A',1,  'numeric','a numeric value indicating the maximum allowed gene set size. Default value is 500.',
+                 "test_method", 'T',1, 'character', "a character parameter indicating which statistical method to use for testing the gene sets. Must be one of 'GSNCAtest', 'WWtest', 'KStest', 'MDtest', 'RKStest', 'RMDtest'.",
+                 "nperm_number", 'N', 1, 'numeric',"number of permutations used to estimate the null distribution of the test statistic. If not given, a default value 1000 is used.",
+                 "cor_method", 'M', 1, 'character',"a character string indicating which correlation coefficient is to be computed. Possible values are 'pearson' (default), 'spearman' and 'kendall'. Default value is 'pearson'.", 
+                 "threshold_value", "V", 1, 'numeric', 'Threshold value for setting significant geneSet.',
+                 "GSAR_output_p_value", 'R', 1, 'character',"P-value table", 
+                 "GSAR_output_plot", 'P', 1, 'character',"Plot genes relationships of significant pathway"
+                 
+),
+byrow = TRUE, ncol = 5)
+
+
+if (!requireNamespace("getopt", quietly = TRUE))
+  install.packages("getopt")
+
+opt <- getopt::getopt(spec)
+
+#----------------
+#整理参数
+#----------------
+# expr_file
+# geneSet_file
+# design_file
+if (is.null(opt$min_size)){min_size = 10}else{min_size = opt$min_size}
+if (is.null(opt$max_size)){max_size = 500}else{max_size = opt$max_size}
+if (is.null(opt$test_method)){test_method = "GSNCAtest"}else{test_method = opt$test_method}
+if (is.null(opt$nperm_number)){nperm_number = 1000}else{nperm_number = opt$nperm_number}
+if (is.null(opt$cor_method)){cor_method = "pearson"}else{cor_method = opt$cor_method}
+if (is.null(opt$threshold_value)){threshold_value = 0.05}else{threshold_value = opt$threshold_value}
+
+
+#================================================================
+#run codes
+#================================================================
+
+#--- load package ------------------
+
+suppressPackageStartupMessages(library(GSAR))
+suppressPackageStartupMessages(library(GSEABase))
+options(stringsAsFactors = FALSE)
+#---input --------------------------
+# expr
+data <- as.matrix(read.csv(opt$expr_file, row.names = 1))
+
+# design
+design <- read.csv(opt$design_file, row.names = 1)
+group <- design$group
+label <- design$label
+
+# geneSet
+load(opt$geneSet_file)
+geneSetlist <- lapply(geneSet, geneIds)
+names(geneSetlist) <- names(geneSet)
+
+#-------GSAR -------------------------
+# test.method <- c("GSNCAtest", "WWtest", "KStest", "MDtest", "RKStest", "RMDtest")
+#  “GSNCAtest”, “WWtest”, “KStest”, “MDtest”, “RKStest”, “RMDtest” 
+results <- TestGeneSets(object=data, group=group, 
+                        geneSets=geneSetlist, min.size=min_size, 
+						max.size=max_size, test=test_method, 
+						nperm = nperm_number)
+
+
+
+#================================================================
+#output
+#================================================================
+
+
+# output p-value----------------------------------------------------
+resutlts1 <- as.data.frame(t(as.data.frame(results)))
+colnames(resutlts1) = "P_value"
+resutlts1$geneSet <- rownames(resutlts1)
+resutlts1 <- resutlts1[,c("geneSet", "P_value")]
+resutlts1 <- resutlts1[order(resutlts1$P_value),]
+write.csv(resutlts1, file = opt$GSAR_output_p_value, row.names = FALSE)
+#-------------------------------------------------------------------
+
+
+
+#plot -------------------------------------------------------------
+sig.paths <- names(results[results  <= threshold_value])
+
+
+group1 <- unique(design[design$group == 1, "label"])
+group2 <- unique(design[design$group == 2, "label"])
+allgenes <- rownames(data)
+
+pdf(file = opt$GSAR_output_plot, width = 10.92)
+if (length(sig.paths) > 0){
+  for (sig.path in sig.paths){
+    path.index <- allgenes %in% geneSetlist[[sig.path]] 
+    ## Plot MST2 for a pathway in two conditions
+    plotMST2.pathway(object=data[path.index,],
+                     group=group, name=sig.path,
+                     legend.size=1.2, #leg.x=-1.2, leg.y=2,
+                     label.size=1, label.dist=0.8, cor.method=cor_method, group1.name = group1, group2.name = group2)
+    
+    rm(sig.path, path.index)
+  }
+  
+}
+dev.off() 
+
+