diff options
| -rw-r--r-- | misc/notes_DA.txt | 10 | ||||
| -rwxr-xr-x | wqflask/base/data_set.py | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/collections/view.html | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/wgcna_results.html | 10 | ||||
| -rwxr-xr-x | wqflask/wqflask/views.py | 13 | ||||
| -rwxr-xr-x | wqflask/wqflask/wgcna/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/wqflask/wgcna/wgcna_analysis.py | 65 |
7 files changed, 110 insertions, 2 deletions
diff --git a/misc/notes_DA.txt b/misc/notes_DA.txt new file mode 100644 index 00000000..410e0182 --- /dev/null +++ b/misc/notes_DA.txt @@ -0,0 +1,10 @@ +Danny's notes about the genenetwork source + +Location of static files: + +Location of HTML templates: wqflask/wqflask/templates/ + +Entry point of the wqflask app: wqflask/wqflask/__init__.py + +Application routes: wqflask/wqflask/views.py + diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index e2db9ad7..427fd991 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -89,7 +89,7 @@ class Dataset_Types(object): for group in data['datasets'][species]: for dataset_type in data['datasets'][species][group]: for dataset in data['datasets'][species][group][dataset_type]: - print("dataset is:", dataset) + #print("dataset is:", dataset) short_dataset_name = dataset[0] if dataset_type == "Phenotypes": diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 29c65058..f3e9f1b9 100755 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -38,6 +38,18 @@ <input type="submit" class="btn btn-primary" value="Correlation Matrix" /> </div> </form> + <form action="/wgcna" method="post"> + {% if uc %} + <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> + {% endif %} + <input type="hidden" name="trait_list" id="trait_list" value= " + {% for this_trait in trait_obs %} + {{ this_trait.name }}:{{ this_trait.dataset.name }}, + {% endfor %}" > + <div class="col-xs-2 controls"> + <input type="submit" class="btn btn-primary" value="WGCNA Analysis" /> + </div> + </form> <form action="/heatmap" method="post"> {% if uc %} <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> diff --git a/wqflask/wqflask/templates/wgcna_results.html b/wqflask/wqflask/templates/wgcna_results.html new file mode 100644 index 00000000..77de3604 --- /dev/null +++ b/wqflask/wqflask/templates/wgcna_results.html @@ -0,0 +1,10 @@ +{% extends "base.html" %} +{% block title %}WCGNA results{% endblock %} + +{% block content %} <!-- Start of body --> + <div> + <h1>WGCNA Results</h1> + Phenotypes used as input: {% for k in result %} {{k[0].name}} {% endfor %} + </div> +{% endblock %} + diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 7a8a0f03..89302120 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -46,6 +46,9 @@ from wqflask.interval_mapping import interval_mapping from wqflask.correlation import show_corr_results from wqflask.correlation_matrix import show_corr_matrix from wqflask.correlation import corr_scatter_plot + +from wqflask.wgcna import wgcna_analysis + from utility import temp_data from base import webqtlFormData @@ -174,6 +177,14 @@ def help(): doc = docs.Docs("help") return render_template("docs.html", **doc.__dict__) +@app.route("/wgcna", methods=('POST',)) +def wcgna(): + print("In wgcna, request.form is:", request.form) + wgcna = wgcna_analysis.WGCNA() # Start R, load the package and pointers and create the analysis + wgcnaA = wgcna.run_analysis(request.form) # Start the analysis, a wgcnaA object should be a separate long running thread + result = wgcna.process_results(wgcnaA) # After the analysis is finished store the result + return render_template("wgcna_results.html", **result) # Display them using the template + @app.route("/news") def news_route(): newsobject = news.News() @@ -328,7 +339,7 @@ def marker_regression_page(): 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno' ) - print("Random Print too see if it is running:", initial_start_vars) + print("Marker regression called with initial_start_vars:", initial_start_vars) start_vars = {} for key, value in initial_start_vars.iteritems(): if key in wanted or key.startswith(('value:')): diff --git a/wqflask/wqflask/wgcna/__init__.py b/wqflask/wqflask/wgcna/__init__.py new file mode 100755 index 00000000..e69de29b --- /dev/null +++ b/wqflask/wqflask/wgcna/__init__.py diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py new file mode 100644 index 00000000..37a37313 --- /dev/null +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -0,0 +1,65 @@ +# WGCNA analysis for GN2 +# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com> + +from numpy import * +import scipy as sp # SciPy +import rpy2.robjects as ro # R Objects + +from utility import helper_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_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 + +class WGCNA(object): + def __init__(self): + print("Initialization of WGCNA") + 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") + self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"] # Map the enableWGCNAThreads function + self.r_pickSoftThreshold = ro.r["pickSoftThreshold"] # Map the pickSoftThreshold function + self.r_blockwiseModules = ro.r["blockwiseModules"] # Map the blockwiseModules function + self.r_labels2colors = ro.r["labels2colors"] # Map the labels2colors function + self.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") + self.r_enableWGCNAThreads() # Enable multi threading + self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] + print("Retrieved phenotype data from database", requestform['trait_list']) + helper_functions.get_trait_db_obs(self, self.trait_db_list) + self.results = {} + for t in self.trait_list: + strains = [] + for s in t[0].data: + strains.append(s) + self.results[t] = strains + + print("Retrieved phenotype data from database") + + def process_results(self, results): + print("Processing WGCNA output") + template_vars = {} + template_vars["result"] = self.results + #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)) + |