diff options
| -rw-r--r-- | wqflask/wqflask/wgcna/wgcna_analysis.py | 39 |
1 files changed, 26 insertions, 13 deletions
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 45c87d3f..5b6c1c1b 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -20,23 +20,36 @@ 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_sink = ro.r["sink"] # Map the sink function +r_file = ro.r["file"] # Map the file 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): - def __init__(self, start_vars): + def __init__(self): print("Initialization of WGCNA") - - def run_wgcna(self): - print("Starting WGCNA analysis") - - def process_wgcna_results(self, results): + log = r_file("/tmp/genenetwork_wcgna.log", open = "wt") + #r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file + #r_sink(log, type = "message") + r_library("WGCNA") # Load WGCNA - Should only be done once, since it is quite expensive + r_options(stringsAsFactors = False) + print("Initialization of WGCNA done, package loaded in R session") + r_enableWGCNAThreads = ro.r["enableWGCNAThreads"] # Map the enableWGCNAThreads function + r_pickSoftThreshold = ro.r["pickSoftThreshold"] # Map the pickSoftThreshold function + r_blockwiseModules = ro.r["blockwiseModules"] # Map the blockwiseModules function + r_labels2colors = ro.r["labels2colors"] # Map the labels2colors function + r_plotDendroAndColors = ro.r["plotDendroAndColors"] # Map the plotDendroAndColors function + print("Obtained pointers to WGCNA functions") + + def run_analysis(self, requestform): + print("Starting WGCNA analysis on dataset") + results = {} + + def process_results(self, results): print("Processing WGCNA output") + template_vars = {} + template_vars["result"] = "OK" + #r_sink(type = "message") # This restores R output to the stdout/stderr + #r_sink() # We should end the Rpy session more or less + return(dict(template_vars)) |