Start R and load the WGCNA library in wgcna_analysis.py

1 files changed, 30 insertions, 0 deletions

diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 824b943c..45c87d3f 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -1,3 +1,33 @@
+# WGCNA analysis for GN2
+# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+
+from numpy import *
+from pandas import *
+
+import scipy as sp                            # SciPy
+import rpy2.robjects as ro                    # R Objects
+import pandas.rpy.common as com               # R common functions
+
+from rpy2.robjects.packages import importr
+utils = importr("utils")
+
+## Get pointers to some common R functions
+r_library       = ro.r["library"]             # Map the library function
+r_options       = ro.r["options"]             # Map the options function
+r_read_csv      = ro.r["read.csv"]            # Map the read.csv function
+r_dim           = ro.r["dim"]                 # Map the dim function
+r_c             = ro.r["c"]                   # Map the c function
+r_seq           = ro.r["seq"]                 # Map the seq function
+r_table         = ro.r["table"]               # Map the table function
+r_names         = ro.r["names"]               # Map the names function
+r_png           = ro.r["png"]                 # Map the png function for plotting
+r_dev_off       = ro.r["dev.off"]             # Map the dev.off function
+
+
+#TODO: This should only be done once, since it is quite expensive
+print(r_library("WGCNA"))                     # Load WGCNA
+print(r_options(stringsAsFactors = False))
+
 
 
 class WGCNA(object):