diff options
| -rw-r--r-- | wqflask/wqflask/auwerx/phewas_analysis.py | 34 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/phewas_analysis.html | 12 |
2 files changed, 39 insertions, 7 deletions
diff --git a/wqflask/wqflask/auwerx/phewas_analysis.py b/wqflask/wqflask/auwerx/phewas_analysis.py index a745b12d..ed2df01f 100644 --- a/wqflask/wqflask/auwerx/phewas_analysis.py +++ b/wqflask/wqflask/auwerx/phewas_analysis.py @@ -5,6 +5,7 @@ from numpy import * import scipy as sp # SciPy import rpy2.robjects as ro # R Objects import rpy2.rinterface as ri +from pprint import pprint from base.webqtlConfig import GENERATED_IMAGE_DIR from utility import webqtlUtil # Random number for the image @@ -17,6 +18,7 @@ import itertools from base import data_set from base import trait as TRAIT +from base.trait import GeneralTrait from utility import helper_functions from utility.tools import locate @@ -29,6 +31,7 @@ r_load = ro.r["load"] # Map the head function r_colnames = ro.r["colnames"] # Map the colnames function r_list = ro.r["list"] # Map the list function r_c = ro.r["c"] # Map the c (combine) function +r_print = ro.r["print"] # Map the c (combine) function r_seq = ro.r["seq"] # Map the rep (repeat) function class PheWAS(object): @@ -46,8 +49,30 @@ class PheWAS(object): def run_analysis(self, requestform): print("Starting PheWAS analysis on dataset") genofilelocation = locate("BXD.geno", "genotype") # Get the location of the BXD genotypes - precompfilelocation = locate("PheWAS_pval_EMMA_norm.RData", "auwerx") # Get the location of the pre-computed EMMA results + precompfile = locate("PheWAS_pval_EMMA_norm.RData", "auwerx") # Get the location of the pre-computed EMMA results + # Get user parameters, trait_id and dataset, and store/update them in self + self.trait_id = requestform["trait_id"] + self.datasetname = requestform["dataset"] + self.dataset = data_set.create_dataset(self.datasetname) + + # Print some debug + print "self.trait_id:" + self.trait_id + "\n" + print "self.datasetname:" + self.datasetname + "\n" + print "self.dataset.type:" + self.dataset.type + "\n" + + # GN Magic ? + self.this_trait = GeneralTrait(dataset=self.dataset, name = self.trait_id, get_qtl_info = False, get_sample_info=False) + pprint(vars(self.this_trait)) + + # Set the values we need + self.chr = str(self.this_trait.chr); + self.mb = int(self.this_trait.mb); + + # print some debug + print "location:" + self.chr + ":" + str(self.mb) + "\n" + + # Load in the genotypes file *sigh* to make the markermap parser = genofile_parser.ConvertGenoFile(genofilelocation) parser.process_csv() snpinfo = [] @@ -71,10 +96,11 @@ class PheWAS(object): print("IMAGE AT:", self.results['imgloc1'] ) # Create the PheWAS plot (The gene/probe name, chromosome and gene/probe positions should come from the user input) # TODO: generate the PDF in the temp folder, with a unique name - phewasres = self.r_PheWASManhattan("Test", precompfilelocation, phenoaligner, snpaligner, "None", 1, 25, 25, self.results['imgloc1'] ) + phewasres = self.r_PheWASManhattan("Test", precompfile, phenoaligner, snpaligner, "None", self.chr, self.mb, self.mb, self.results['imgloc1'] ) self.results['phewas1'] = phewasres[0] self.results['phewas2'] = phewasres[1] - self.results['phewas3'] = phewasres[2] + self.results['tabulardata'] = phewasres[2] + self.results['R_debuglog'] = phewasres[3] #self.r_PheWASManhattan(allpvalues) #self.r_Stop() @@ -98,5 +124,7 @@ class PheWAS(object): template_vars = {} template_vars["results"] = self.results self.render_image(self.results) + template_vars["R_debuglog"] = self.results['R_debuglog'] + return(dict(template_vars)) diff --git a/wqflask/wqflask/templates/phewas_analysis.html b/wqflask/wqflask/templates/phewas_analysis.html index fbe7c364..4dbc071f 100644 --- a/wqflask/wqflask/templates/phewas_analysis.html +++ b/wqflask/wqflask/templates/phewas_analysis.html @@ -4,17 +4,21 @@ {% block content %} <!-- Start of body --> <div class="container"> <h1>PheWAS analysis results</h1> + <h3>R debug log</h3> + {% for i in range(results['R_debuglog']|length) %} + {{ results['R_debuglog'][i]}}<br> + {%- endfor %} <h2>Top 5 PheWAS hits</h2> <table width="100%"> <tr><th>GN ID</th><th>Phenotype</th><th>Phenosome</th><th>LOD</th></tr> {% for r in range(5) %} <tr> - {% for c in range(results['phewas3']|length) %} + {% for c in range(results['tabulardata']|length) %} <td> - {% if c == 4 %} - {{results['phewas3'][c][r]|float|round(2)}} + {% if c == 3 %} + {{results['tabulardata'][c][r]|float|round(2)}} {% else %} - {{results['phewas3'][c][r]}} + {{results['tabulardata'][c][r]}} {% endif %} </td> {%- endfor %} |