debug if 2 library

bin/Normalization.R

@@ -10,7 +10,7 @@ packages <- c("optparse", # to read arguments from a command line
 for(package in packages){
   # if package is installed locally, load
   if (!(package %in% rownames(installed.packages()))) {
-    install.packages(package)
+    install.packages(package, repos="http://cran.univ-paris1.fr")
   }
   do.call('library', list(package))
 } 
@@ -100,14 +100,16 @@ ggsave(filename = normalizePath(file.path(opt$out, "rawcount_boxplot.svg"),
                                 mustWork = FALSE), width = 11, height = 7)
 
 ## MDS
-MDS_PC <- data.frame(plotMDS(PC_before_log)$cmdscale.out)
-
-ggplot(MDS_PC, aes(x = X1, y = X2, label = rownames(MDS_PC))) + 
-  geom_point(size=4) + geom_text(hjust=0.5, vjust=-0.5) + theme_bw() + 
-  xlab(label = "Dimension 1") + ylab(label = "Dimension 2") + 
-  ggtitle("PCA plot on raw pseudo-counts")
-ggsave(filename = normalizePath(file.path(opt$out, "rawcount_MDS.svg"), 
-                                mustWork = FALSE), width = 11, height = 7)
+if (ncol(PC_before) > 2){
+  MDS_PC <- data.frame(plotMDS(PC_before_log)$cmdscale.out)
+
+  ggplot(MDS_PC, aes(x = X1, y = X2, label = rownames(MDS_PC))) + 
+    geom_point(size=4) + geom_text(hjust=0.5, vjust=-0.5) + theme_bw() + 
+    xlab(label = "Dimension 1") + ylab(label = "Dimension 2") + 
+    ggtitle("PCA plot on raw pseudo-counts")
+  ggsave(filename = normalizePath(file.path(opt$out, "rawcount_MDS.svg"), 
+                                  mustWork = FALSE), width = 11, height = 7)
+}
 
 ## density
 ggplot(PC_before_log_long, aes(x=log2CPM, colour=lib)) + geom_density() + 
@@ -124,9 +126,12 @@ write.table(PC_before_log_long, file = normalizePath(file.path(opt$out,
                                                     "raw_boxplot_density.csv"), 
                                                     mustWork = FALSE), sep = "\t", 
             row.names = TRUE, quote = FALSE)
-write.table(MDS_PC, file = normalizePath(file.path(opt$out, "raw_MDS.csv"), 
+
+if (ncol(PC_before) > 2){
+  write.table(MDS_PC, file = normalizePath(file.path(opt$out, "raw_MDS.csv"), 
                                          mustWork = FALSE), sep = "\t", 
             row.names = TRUE, quote = FALSE)
+}
 
 
 #######################################
@@ -209,10 +214,12 @@ normalization <- function(dge, method) {
                                           paste0(method, "_boxplot_density.csv")), 
                                           mustWork = FALSE), sep = "\t", 
               row.names = TRUE, quote = FALSE)
-  write.table(MDS_PC, file = normalizePath(file.path(opt$out, 
+  if (ncol(PC_before) > 2){
+    write.table(MDS_PC, file = normalizePath(file.path(opt$out, 
                                                     paste0(method, "_MDS.csv")), 
                                            mustWork = FALSE), sep = "\t", 
               row.names = TRUE, quote = FALSE)
+  }
 }
 
 normalization(dge, "upperquartile")