diff options
| -rw-r--r-- | wqflask/wqflask/auwerx/phewas_analysis.py | 11 |
1 files changed, 6 insertions, 5 deletions
diff --git a/wqflask/wqflask/auwerx/phewas_analysis.py b/wqflask/wqflask/auwerx/phewas_analysis.py index db12ad98..a745b12d 100644 --- a/wqflask/wqflask/auwerx/phewas_analysis.py +++ b/wqflask/wqflask/auwerx/phewas_analysis.py @@ -59,14 +59,11 @@ class PheWAS(object): rnames = r_seq(1, len(parser.markers)) # Create the snp aligner object out of the BXD genotypes snpaligner = ro.r.matrix(snpinfo, nrow=len(parser.markers), dimnames = r_list(rnames, r_c("SNP", "Chr", "Pos")), ncol = 3, byrow=True) - r_write_table(snpaligner, "~/snpaligner_GN2.txt", row_names=False) + #r_write_table(snpaligner, "~/snpaligner_GN2.txt", row_names=False) # Create the phenotype aligner object using R phenoaligner = self.r_create_Pheno_aligner() - #r_load(precompfilelocation) # Load the pre-computed EMMA results into R - #allpvalues = ro.r['pval_small'] # Get a pointer to the pre-computed results - self.results = {} self.results['imgurl1'] = webqtlUtil.genRandStr("phewas_") + ".png" self.results['imgloc1'] = GENERATED_IMAGE_DIR + self.results['imgurl1'] @@ -74,7 +71,11 @@ 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 - self.r_PheWASManhattan("Test", precompfilelocation, phenoaligner, snpaligner, "None", 1, 25, 25, self.results['imgloc1'] ) + phewasres = self.r_PheWASManhattan("Test", precompfilelocation, phenoaligner, snpaligner, "None", 1, 25, 25, self.results['imgloc1'] ) + self.results['phewas1'] = phewasres[0] + self.results['phewas2'] = phewasres[1] + self.results['phewas3'] = phewasres[2] + #self.r_PheWASManhattan(allpvalues) #self.r_Stop() |