diff options
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 70 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_calculate_correlations.html | 1 |
2 files changed, 49 insertions, 22 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index be27da7b..0654e5d3 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -34,6 +34,11 @@ import json import scipy import numpy +import rpy2.robjects as ro # R Objects +import rpy2.rinterface as ri + +from rpy2.robjects.packages import importr +utils = importr("utils") from pprint import pformat as pf @@ -258,6 +263,8 @@ class CorrelationResults(object): self.formatted_corr_type += "(Pearson's r)" elif self.corr_method == "spearman": self.formatted_corr_type += "(Spearman's rho)" + elif self.corr_method == "bicor": + self.formatted_corr_type += "(Biweight r)" def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1): """Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each""" @@ -446,7 +453,9 @@ class CorrelationResults(object): self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ - if self.corr_method == 'pearson': + if self.corr_method == 'bicor': + sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals) + elif self.corr_method == 'pearson': sample_r, sample_p = scipy.stats.pearsonr(self.this_trait_vals, target_vals) else: sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals) @@ -469,6 +478,22 @@ class CorrelationResults(object): if not value.strip().lower() == 'x': self.sample_data[str(sample)] = float(value) +def do_bicor(this_trait_vals, target_trait_vals): + r_library = ro.r["library"] # Map the library function + r_options = ro.r["options"] # Map the options function + + r_library("WGCNA") + r_bicor = ro.r["bicorAndPvalue"] # Map the bicorAndPvalue function + + r_options(stringsAsFactors = False) + + this_vals = ro.Vector(this_trait_vals) + target_vals = ro.Vector(target_trait_vals) + + the_r, the_p, _fisher_transform, _the_t, _n_obs = [numpy.asarray(x) for x in r_bicor(x = this_vals, y = target_vals)] + + return the_r, the_p + def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api = False): results_list = [] for i, trait in enumerate(corr_results): @@ -549,19 +574,19 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap def get_header_fields(data_type, corr_method): if data_type == "ProbeSet": - if corr_method == "pearson": + if corr_method == "spearman": header_fields = ['Index', 'Record', 'Symbol', 'Description', 'Location', 'Mean', - 'Sample r', + 'Sample rho', 'N', - 'Sample p(r)', - 'Lit r', - 'Tissue r', - 'Tissue p(r)', + 'Sample p(rho)', + 'Lit rho', + 'Tissue rho', + 'Tissue p(rho)', 'Max LRS', 'Max LRS Location', 'Additive Effect'] @@ -572,25 +597,25 @@ def get_header_fields(data_type, corr_method): 'Description', 'Location', 'Mean', - 'Sample rho', + 'Sample r', 'N', - 'Sample p(rho)', - 'Lit rho', - 'Tissue rho', - 'Tissue p(rho)', + 'Sample p(r)', + 'Lit r', + 'Tissue r', + 'Tissue p(r)', 'Max LRS', 'Max LRS Location', 'Additive Effect'] elif data_type == "Publish": - if corr_method == "pearson": + if corr_method == "spearman": header_fields = ['Index', 'Record', 'Description', 'Authors', 'Year', - 'Sample r', + 'Sample rho', 'N', - 'Sample p(r)', + 'Sample p(rho)', 'Max LRS', 'Max LRS Location', 'Additive Effect'] @@ -600,26 +625,27 @@ def get_header_fields(data_type, corr_method): 'Description', 'Authors', 'Year', - 'Sample rho', + 'Sample r', 'N', - 'Sample p(rho)', + 'Sample p(r)', 'Max LRS', 'Max LRS Location', 'Additive Effect'] + else: - if corr_method == "pearson": + if corr_method == "spearman": header_fields = ['Index', 'ID', 'Location', - 'Sample r', + 'Sample rho', 'N', - 'Sample p(r)'] + 'Sample p(rho)'] else: header_fields = ['Index', 'ID', 'Location', - 'Sample rho', + 'Sample r', 'N', - 'Sample p(rho)'] + 'Sample p(r)'] return header_fields
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 8ceec4fa..297d62ce 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -70,6 +70,7 @@ <select name="corr_sample_method" class="form-control"> <option value="pearson">Pearson</option> <option value="spearman">Spearman Rank</option> + <option value="bicor">Biweight Midcorrelation</option> </select> </div> </div> |