From bb1f1608edb23d5e5be16b5c4573d7696d985aff Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 5 May 2020 15:17:52 +0300 Subject: Use GUIX javascript Datatables package --- wqflask/wqflask/templates/admin/group_manager.html | 2 +- wqflask/wqflask/templates/collections/list.html | 2 +- wqflask/wqflask/templates/collections/view.html | 2 +- wqflask/wqflask/templates/correlation_matrix.html | 2 +- wqflask/wqflask/templates/correlation_page.html | 2 +- wqflask/wqflask/templates/gsearch_gene.html | 2 +- wqflask/wqflask/templates/gsearch_pheno.html | 2 +- wqflask/wqflask/templates/mapping_results.html | 2 +- wqflask/wqflask/templates/pair_scan_results.html | 2 +- wqflask/wqflask/templates/search_result_page.html | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index ea9026a6..1c536cb2 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -46,7 +46,7 @@ {% block js %} - + diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index 3829b950..34224d68 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -66,7 +66,7 @@ {% block js %} - + diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 6639f46a..f7065cdb 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -166,7 +166,7 @@ - + diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 9af52021..2a207c80 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -135,7 +135,7 @@ - + - + diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 556d46d3..555f9aa1 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -48,7 +48,7 @@ {% block js %} - + diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index f6ffff47..ed892ec0 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -48,7 +48,7 @@ {% block js %} - + diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 7e05be18..a1ea6d89 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -333,7 +333,7 @@ - + diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html index 1ccb2b27..38c0489c 100644 --- a/wqflask/wqflask/templates/pair_scan_results.html +++ b/wqflask/wqflask/templates/pair_scan_results.html @@ -65,7 +65,7 @@ - + diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 0f5c39b0..3cd51e2e 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -152,7 +152,7 @@ - + -- cgit v1.2.3 From 8df6a19e487e31dfa4a184444e8eace11cda9b15 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 6 May 2020 01:24:36 +0300 Subject: Replace CSS dependencies for datatables --- wqflask/utility/tools.py | 2 +- wqflask/wqflask/templates/collections/list.html | 2 +- wqflask/wqflask/templates/collections/view.html | 2 +- wqflask/wqflask/templates/corr_scatterplot.html | 2 +- wqflask/wqflask/templates/correlation_matrix.html | 2 +- wqflask/wqflask/templates/correlation_page.html | 2 +- wqflask/wqflask/templates/gsearch_gene.html | 2 +- wqflask/wqflask/templates/gsearch_pheno.html | 2 +- wqflask/wqflask/templates/mapping_results.html | 2 +- wqflask/wqflask/templates/pair_scan_results.html | 2 +- wqflask/wqflask/templates/search_error.html | 2 +- wqflask/wqflask/templates/search_result_page.html | 2 +- wqflask/wqflask/templates/show_trait.html | 2 +- wqflask/wqflask/templates/snp_browser.html | 2 +- 14 files changed, 14 insertions(+), 14 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 2914d354..89d88516 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -292,7 +292,7 @@ JS_GUIX_PATH = get_setting("JS_GUIX_PATH") assert_dir(JS_GUIX_PATH) assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') -CSS_PATH = "UNKNOWN" +CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS # assert_dir(JS_PATH) JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher")) diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index 34224d68..c8705c7d 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Your Collections{% endblock %} {% block css %} - + {% endblock %} diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index f7065cdb..34734a01 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}View Collection{% endblock %} {% block css %} - + {% endblock %} diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html index ffc8244d..5877e367 100644 --- a/wqflask/wqflask/templates/corr_scatterplot.html +++ b/wqflask/wqflask/templates/corr_scatterplot.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block css %} - + diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 2a207c80..cb9fb815 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -1,6 +1,6 @@ {% extends "base.html" %} {% block css %} - + diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index c4782bb9..b696a3fa 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -1,6 +1,6 @@ {% extends "base.html" %} {% block css %} - + {% endblock %} diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 555f9aa1..8c261eec 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Search Results{% endblock %} {% block css %} - + {% endblock %} {% block content %} diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index ed892ec0..05b2f988 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Search Results{% endblock %} {% block css %} - + {% endblock %} {% block content %} diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index a1ea6d89..8699343f 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Mapping Results{% endblock %} {% block css %} - + diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html index 38c0489c..b13b393f 100644 --- a/wqflask/wqflask/templates/pair_scan_results.html +++ b/wqflask/wqflask/templates/pair_scan_results.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Pair Scan{% endblock %} {% block css %} - + diff --git a/wqflask/wqflask/templates/search_error.html b/wqflask/wqflask/templates/search_error.html index 7399b377..df8d9dff 100644 --- a/wqflask/wqflask/templates/search_error.html +++ b/wqflask/wqflask/templates/search_error.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Search Results{% endblock %} {% block css %} - + {% endblock %} {% block content %} diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 3cd51e2e..767e3487 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Search Results{% endblock %} {% block css %} - + diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 27c3e398..d29be30b 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -6,7 +6,7 @@ - + diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html index 4422ba73..88cb4d31 100644 --- a/wqflask/wqflask/templates/snp_browser.html +++ b/wqflask/wqflask/templates/snp_browser.html @@ -1,6 +1,6 @@ {% extends "base.html" %} {% block css %} - + -- cgit v1.2.3 From bcd0110bbf8d3e290023891852c21de3d5b7ebc6 Mon Sep 17 00:00:00 2001 From: Danny Arends Date: Wed, 6 May 2020 12:06:40 -0500 Subject: Put in TODOs for MariaDB query and Design Matrix --- wqflask/wqflask/marker_regression/rqtl_mapping.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 152bb5be..4070e9f5 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -62,6 +62,7 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers logger.info("Marker covars done"); if cofactors != "": + logger.info("Cofactors: " + cofactors); cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits ro.r('all_covars <- cbind(marker_covars, trait_covars)') else: @@ -71,7 +72,6 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe #logger.info("Saving Done"); covars = ro.r['all_covars'] #DEBUG to save the session object to file - #ro.r('save.image(file = "/home/dannya/gn2-danny/all.RData")') if pair_scan: if do_control == "true": logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16) @@ -274,7 +274,8 @@ def add_cofactors(cross, this_dataset, covariates, samples): covar_name_string += ")" covars_ob = pull_var("trait_covars", cross, covar_name_string) - + # TODO: Pull in the types of the covars from MariaDB + # TODO: Iterate through the covar types and create a design matrix based on it return cross, covars_ob def create_marker_covariates(control_marker, cross): @@ -287,7 +288,7 @@ def create_marker_covariates(control_marker, cross): ro.r('covnames <- covnames[covInGeno]') ro.r("cat('covnames (purged): ', covnames,'\n')") ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file - + # TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc return ro.r["marker_covars"] def process_pair_scan_results(result): -- cgit v1.2.3 From 74ddd3556a838fd48c425a73d76d504996fb3644 Mon Sep 17 00:00:00 2001 From: Danny Arends Date: Tue, 12 May 2020 06:57:58 -0500 Subject: Mapping Rqtl using the correct way to use categorical covars --- wqflask/wqflask/marker_regression/rqtl_mapping.py | 79 ++++++++++++++++++++--- 1 file changed, 71 insertions(+), 8 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 4070e9f5..f3d9a70e 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -1,16 +1,36 @@ import rpy2.robjects as ro import rpy2.robjects.numpy2ri as np2r import numpy as np +import json from base.webqtlConfig import TMPDIR from base.trait import GeneralTrait from base.data_set import create_dataset from utility import webqtlUtil from utility.tools import locate, TEMPDIR +from flask import g import utility.logger logger = utility.logger.getLogger(__name__ ) +# Get a trait's type (numeric, categorical, etc) from the DB +def get_trait_data_type(trait_db_string): + logger.info("get_trait_data_type"); + the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'" + logger.info("the_query done"); + results_json = g.db.execute(the_query).fetchone() + logger.info("the_query executed"); + results_ob = json.loads(results_json[0]) + logger.info("json results loaded"); + if trait_db_string in results_ob: + logger.info("found"); + return results_ob[trait_db_string] + else: + logger.info("not found"); + return "numeric" + + +# Run qtl mapping using R/qtl def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors): logger.info("Start run_rqtl_geno"); ## Get pointers to some common R functions @@ -63,7 +83,7 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe logger.info("Marker covars done"); if cofactors != "": logger.info("Cofactors: " + cofactors); - cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits + cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits ro.r('all_covars <- cbind(marker_covars, trait_covars)') else: ro.r('all_covars <- marker_covars') @@ -218,6 +238,34 @@ def add_phenotype(cross, pheno_as_string, col_name): ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric('+ pheno_as_string +'))') return ro.r["the_cross"] +def add_categorical_covar(cross, covar_as_string, i): + ro.globalenv["the_cross"] = cross + logger.info("cross set"); + ro.r('covar <- as.factor(' + covar_as_string + ')') + logger.info("covar set"); + ro.r('newcovar <- model.matrix(~covar-1)') + logger.info("model.matrix finished"); + ro.r('cat("new covar columns", ncol(newcovar), "\n")') + nCol = ro.r('ncol(newcovar)') + logger.info("ncol covar done: " + str(nCol[0])); + ro.r('pheno <- data.frame(pull.pheno(the_cross))') + logger.info("pheno pulled from cross"); + nCol = int(nCol[0]) + logger.info("nCol python int:" + str(nCol)); + col_names = [] + #logger.info("loop") + for x in range(1, (nCol+1)): + #logger.info("loop" + str(x)); + col_name = "covar_" + str(i) + "_" + str(x) + #logger.info("col_name" + col_name); + ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = newcovar[,' + str(x) + '])') + col_names.append(col_name) + #logger.info("loop" + str(x) + "done"); + + logger.info("returning from add_categorical_covar"); + return ro.r["the_cross"], col_names + + def add_names(cross, names_as_string, col_name): ro.globalenv["the_cross"] = cross ro.r('pheno <- data.frame(pull.pheno(the_cross))') @@ -236,6 +284,7 @@ def add_cofactors(cross, this_dataset, covariates, samples): covariate_list = covariates.split(",") covar_name_string = "c(" for i, covariate in enumerate(covariate_list): + logger.info("Covariate: " + covariate); this_covar_data = [] covar_as_string = "c(" trait_name = covariate.split(":")[0] @@ -263,19 +312,33 @@ def add_cofactors(cross, this_dataset, covariates, samples): covar_as_string += ")" - col_name = "covar_" + str(i) - cross = add_phenotype(cross, covar_as_string, col_name) + datatype = get_trait_data_type(covariate) + logger.info("Covariate: " + covariate + " is of type: " + datatype); + if(datatype == "categorical"): # Cat variable + logger.info("call of add_categorical_covar"); + cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross + logger.info("add_categorical_covar returned"); + for z, col_name in enumerate(col_names): # Go through the additional covar names + if i < (len(covariate_list) - 1): + covar_name_string += '"' + col_name + '", ' + else: + if(z < (len(col_names) -1)): + covar_name_string += '"' + col_name + '", ' + else: + covar_name_string += '"' + col_name + '"' - if i < (len(covariate_list) - 1): - covar_name_string += '"' + col_name + '", ' + logger.info("covar_name_string:" + covar_name_string); else: + col_name = "covar_" + str(i) + cross = add_phenotype(cross, covar_as_string, col_name) + if i < (len(covariate_list) - 1): + covar_name_string += '"' + col_name + '", ' + else: covar_name_string += '"' + col_name + '"' covar_name_string += ")" - + logger.info("covar_name_string:" + covar_name_string); covars_ob = pull_var("trait_covars", cross, covar_name_string) - # TODO: Pull in the types of the covars from MariaDB - # TODO: Iterate through the covar types and create a design matrix based on it return cross, covars_ob def create_marker_covariates(control_marker, cross): -- cgit v1.2.3