From e5992ce3e047fcfe79d66ed42c00c1af63438482 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 15 Mar 2018 17:59:35 +0000 Subject: Resolved conflicts --- .../wqflask/correlation_matrix/show_corr_matrix.py | 9 +- .../wqflask/marker_regression/marker_regression.py | 1 + .../marker_regression/marker_regression_gn1.py | 2 + .../wqflask/marker_regression/qtlreaper_mapping.py | 17 +- wqflask/wqflask/templates/correlation_matrix.html | 3 +- .../show_trait_calculate_correlations.html | 106 ++++++------ .../templates/show_trait_mapping_tools.html | 185 ++++++++++++++++++++- wqflask/wqflask/views.py | 2 +- 8 files changed, 250 insertions(+), 75 deletions(-) diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index b34beb7b..077386a3 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -173,9 +173,12 @@ class CorrelationMatrix(object): for sample in self.all_sample_list: groups.append(1) - pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) - - self.loadings_array = self.process_loadings() + try: + self.pca_works = "True" + pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) + self.loadings_array = self.process_loadings() + except: + self.pca_works = "False" self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 087b95b4..db4f8f46 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -228,6 +228,7 @@ class MarkerRegression(object): results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait, self.dataset, self.samples, + self.vals, self.json_data, self.num_perm, self.bootCheck, diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 211cf187..66884b0c 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -1204,6 +1204,8 @@ class MarkerRegression(object): else: if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": string2 = 'Using GEMMA mapping method with no control for other QTLs.' + if self.covariates != "": + string3 = 'Using following traits as covariates: ' + self.covariates elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": string2 = 'Using R/qtl mapping method with no control for other QTLs.' elif self.mapping_method == "plink": diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 50228b5e..6b58190f 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -1,17 +1,20 @@ -def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): genotype = dataset.group.read_genotype_file() if manhattan_plot != True: genotype = genotype.addinterval() - samples, values, variances, sample_aliases = this_trait.export_informative() - trimmed_samples = [] trimmed_values = [] - for i in range(0, len(samples)): - if this_trait.data[samples[i]].name in samples_before: - trimmed_samples.append(samples[i]) - trimmed_values.append(values[i]) + for i in range(0, len(samples_before)): + try: + trimmed_values.append(float(trait_vals[i])) + trimmed_samples.append(samples_before[i]) + except: + pass perm_output = [] bootstrap_results = [] diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index ab793d58..d27788a8 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -61,6 +61,7 @@
+{% if pca_works == "True" %}

Factor Loadings Plot

@@ -93,7 +94,7 @@ - +{% endif %} {% endblock %} {% block js %} diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index c5f815ce..ef233333 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -1,9 +1,10 @@
+
- -
+ +
{% for tissue in corr_tools.dataset_menu %} {% if tissue.tissue %} @@ -37,8 +38,8 @@
- -
+ +
{% for group, pretty_group in sample_group_types.items() %} @@ -64,8 +65,8 @@
- -
+ +
- -
+ +
Chr:     Mb:  to  @@ -89,8 +90,8 @@
- -
+ +
@@ -103,48 +104,45 @@
- -
+ +
- -
- -
- - The Sample Correlation - is computed - between trait data and any - other traits in the sample database selected above. Use - Spearman - Rank - when the sample size is small (<20) or when there are influential outliers. - - - -
-
+
+
+ + The Sample Correlation + is computed + between trait data and any + other traits in the sample database selected above. Use + Spearman + Rank + when the sample size is small (<20) or when there are influential outliers. + + + +
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index dcec2b9e..60219cf5 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,6 +1,11 @@
+<<<<<<< HEAD {% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %}
+======= + {% if dataset.group.mapping_names|length > 0 %} +
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    @@ -41,8 +46,13 @@
    {% if genofiles and genofiles|length>0 %}
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    + +
    + + {% endif %} +
    +
    +
    + +
    +
    @@ -94,8 +139,13 @@
    {% if genofiles and genofiles|length>0 %}
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -162,8 +227,13 @@
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= +
    + +
    + +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    @@ -189,8 +268,13 @@
    {% if genofiles and genofiles|length>0 %}
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page +======= + +
    + +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -228,8 +323,13 @@
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= +
    + +
    + +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    @@ -295,8 +414,13 @@
    {% if genofiles and genofiles|length>0 %}
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page