pca plot with no colors, ref #13

PCAPlot.R

@@ -6,40 +6,41 @@
 #
 
 suppressPackageStartupMessages(library(argparse))
-library(devtools)
-install_github("ggbiplot", "vqv")
-library(ggbiplot)
+suppressPackageStartupMessages(library(ggbiplot))
 
-parser <- ArgumentParser(description="Plot PCA")
-parser$add_argument("--matrix", required=TRUE, help="normalized expression matrix output")
+parser <- ArgumentParser(description="Plot PCA from a matrix file.")
+parser$add_argument("--matrix", required=TRUE, help="matrix file")
 parser$add_argument("--pdf", required=TRUE, help="path to PDF output")
 args   <- parser$parse_args()
 
 
 pcaexprmat<-function(M){
-        #An expression matrix as input.
-        T.M<-t(M)
-        #Se transpone para que los pacientes queden como rownames y se integren con los grupos definidos sobre ellossean grupo
-        colnames(T.M)<-rownames(M)
-        # Se evita que los colnames de la nueva matrix queden vacios (de lo contrario ggplots dara problemas)
-        T.M.log<-log(T.M)
-        T.M.pca<-prcomp(T.M,center=TRUE,scale.=TRUE)
-        summary(T.M.pca)
-        plot(T.M.pca, type = "l")
-        return(T.M.pca)
+    T.M<-t(M)
+    colnames(T.M)<-rownames(M)
+    T.M.log<-log(T.M)
+    T.M.pca<-prcomp(T.M, center=TRUE, scale.=TRUE)
+                                        #plot(T.M.pca, type = "l")
+
+    summary(T.M.pca)
+    return(T.M.pca)
 }
 
 
-plotpcagroups <-function (T.M.pca , SPECIES){
-              g <- ggbiplot(T.M.pca, obs.scale = 1, var.scale = 1, var.axes=FALSE ,groups = SPECIES, ellipse = TRUE, circle = TRUE)
-              g <- g + scale_color_discrete(name = '')
-              g <- g + theme(legend.direction = 'horizontal',
-               legend.position = 'top')
-               pdf(file="PlotT.M.pca.pdf")
-               print(g)
-               dev.off()
+plotpcagroups <-function (T.M.pca, outpdf) {
+    pdf(file=outpdf)    
+    g <- ggbiplot(T.M.pca, obs.scale = 1, var.scale = 1, var.axes=FALSE, ellipse = TRUE, circle = TRUE)
+    g <- g + scale_color_discrete(name = '')
+    g <- g + theme(legend.direction = 'horizontal',
+                   legend.position = 'top')
+    print(g)
+    dev.off()
 }
 
 
-M = read.table(args$matrix)
-plotpcagroups( pcaexprmat(M) )
+
+
+
+
+M = read.table(args$matrix, sep=",", header=TRUE, row.names=1)
+
+plotpcagroups( pcaexprmat(M), args$pdf )