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-rw-r--r--wqflask/utility/gen_geno_ob.py4
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py36
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py116
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py4
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js7
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html18
6 files changed, 140 insertions, 45 deletions
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index aa5b27c4..db40f6ea 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -45,10 +45,12 @@ class genotype(object):
chr_ob = None
for marker in qtl_results:
locus = Locus(self)
- if str(marker['chr']) != this_chr:
+ if (str(marker['chr']) != this_chr) and this_chr != "X": #ZS: This is really awkward but works as a temporary fix
if this_chr != "":
self.chromosomes.append(chr_ob)
this_chr = str(marker['chr'])
+ if this_chr == "20":
+ this_chr = "X"
chr_ob = Chr(this_chr, self)
if 'chr' in marker:
locus.chr = str(marker['chr'])
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 302a4ff9..b8f84721 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -334,6 +334,10 @@ class DisplayMappingResults(object):
################################################################
self.ChrList = [("All", -1)]
for i, indChr in enumerate(self.genotype):
+ if self.dataset.group.species == "mouse" and indChr.name == "20":
+ self.ChrList.append(("X", i))
+ elif self.dataset.group.species == "rat" and indChr.name == "21":
+ self.ChrList.append(("X", i))
self.ChrList.append((indChr.name, i))
self.ChrLengthMbList = g.db.execute("""
@@ -356,10 +360,7 @@ class DisplayMappingResults(object):
self.ChrLengthCMList = []
for i, _chr in enumerate(self.genotype):
- if self.mapping_method == "rqtl_geno" and self.genotype.filler == True:
- self.ChrLengthCMList.append(_chr[-1].cM)
- else:
- self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
+ self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)
@@ -1568,10 +1569,7 @@ class DisplayMappingResults(object):
if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
for i, _chr in enumerate(self.genotype):
thisChr = []
- if self.mapping_method == "rqtl_geno" and self.genotype.filler == True:
- Locus0CM = 0
- else:
- Locus0CM = _chr[0].cM
+ Locus0CM = _chr[0].cM
nLoci = len(_chr)
if nLoci <= 8:
for _locus in _chr:
@@ -1593,10 +1591,7 @@ class DisplayMappingResults(object):
for i, _chr in enumerate(self.genotype):
if _chr.name == self.ChrList[self.selectedChr][0]:
thisChr = []
- if self.mapping_method == "rqtl_geno" and self.genotype.filler == True:
- Locus0CM = 0
- else:
- Locus0CM = _chr[0].cM
+ Locus0CM = _chr[0].cM
for _locus in _chr:
if _locus.name != ' - ':
if _locus.cM != preLpos:
@@ -1892,12 +1887,21 @@ class DisplayMappingResults(object):
oldStartPosX = newStartPosX
#ZS: This is beause the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used
- if self.plotScale == "physic":
- this_chr = str(self.ChrList[self.selectedChr][0])
- else:
+ this_chr = str(self.ChrList[self.selectedChr][0])
+ if self.plotScale != "physic":
this_chr = str(self.ChrList[self.selectedChr][1]+1)
+
if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
- Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+ if self.plotScale != "physic" and self.genotype.filler == True:
+ if self.selectedChr != -1:
+ start_cm = self.genotype[self.selectedChr - 1][0].cM
+ Xc = startPosX + (qtlresult['Mb'] - start_cm)*plotXScale
+ else:
+ start_cm = self.genotype[previous_chr_as_int][0].cM
+ Xc = startPosX + ((qtlresult['Mb']-start_cm-startMb)*plotXScale)*(((qtlresult['Mb']-start_cm-startMb)*plotXScale)/((qtlresult['Mb']-start_cm-startMb+self.GraphInterval)*plotXScale))
+ else:
+ Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+
# updated by NL 06-18-2011:
# fix the over limit LRS graph issue since genotype trait may give infinite LRS;
# for any lrs is over than 460(LRS max in this system), it will be reset to 460
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 2e3ea406..d76f3812 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -1,14 +1,17 @@
import rpy2.robjects as ro
+import rpy2.robjects.numpy2ri as np2r
import numpy as np
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
import utility.logger
logger = utility.logger.getLogger(__name__ )
-def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control, control_marker, manhattan_plot, pair_scan):
+def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control, control_marker, manhattan_plot, pair_scan, samples, cofactors):
## Get pointers to some common R functions
r_library = ro.r["library"] # Map the library function
r_c = ro.r["c"] # Map the c function
@@ -43,14 +46,22 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
else:
cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
- cross_object = add_phenotype(cross_object, sanitize_rqtl_phenotype(vals)) # Add the phenotype
+ cross_object = add_phenotype(cross_object, sanitize_rqtl_phenotype(vals), "the_pheno") # Add the phenotype
# Scan for QTLs
- covar = create_covariates(control_marker, cross_object) # Create the additive covariate matrix
+ marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
+
+ if 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:
+ ro.r('all_covars <- marker_covars')
+
+ covars = ro.r['all_covars']
if pair_scan:
if do_control == "true":
- logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method, n_cluster = 16)
+ logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
else:
logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
@@ -61,14 +72,14 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
return process_pair_scan_results(result_data_frame)
else:
- if do_control == "true":
- logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method)
+ if do_control == "true" or cofactors != "":
+ logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method)
else:
logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user)
- if do_control == "true":
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = num_perm, model=model, method=method)
+ if do_control == "true" or cofactors != "":
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = num_perm, model=model, method=method)
else:
perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
@@ -118,23 +129,6 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
}
""" % (dataset.group.name + ".geno"))
-def add_phenotype(cross, pheno_as_string):
- ro.globalenv["the_cross"] = cross
- ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), the_pheno = '+ pheno_as_string +')')
- return ro.r["the_cross"]
-
-def create_covariates(control_marker, cross):
- ro.globalenv["the_cross"] = cross
- ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
- userinputS = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
- covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
- ro.r('covnames <- c(' + covariate_names + ')')
- ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
- ro.r('covnames <- covnames[covInGeno]')
- ro.r("cat('covnames (purged): ', covnames,'\n')")
- ro.r('covariates <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
- return ro.r["covariates"]
-
def sanitize_rqtl_phenotype(vals):
pheno_as_string = "c("
for i, val in enumerate(vals):
@@ -151,6 +145,78 @@ def sanitize_rqtl_phenotype(vals):
pheno_as_string += ")"
return pheno_as_string
+def add_phenotype(cross, pheno_as_string, col_name):
+ ro.globalenv["the_cross"] = cross
+ ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), ' + col_name + ' = '+ pheno_as_string +')')
+ return ro.r["the_cross"]
+
+def pull_covar(cross, covar_name_string):
+ ro.globalenv["the_cross"] = cross
+ ro.r('trait_covars <- pull.pheno(the_cross, ' + covar_name_string + ')')
+
+ return ro.r["trait_covars"]
+
+def add_cofactors(cross, this_dataset, covariates, samples):
+ ro.numpy2ri.activate()
+
+ covariate_list = covariates.split(",")
+ covar_name_string = "c("
+ for i, covariate in enumerate(covariate_list):
+ this_covar_data = []
+ covar_as_string = "c("
+ trait_name = covariate.split(":")[0]
+ dataset_ob = create_dataset(covariate.split(":")[1])
+ trait_ob = GeneralTrait(dataset=dataset_ob,
+ name=trait_name,
+ cellid=None)
+
+ this_dataset.group.get_samplelist()
+ trait_samples = this_dataset.group.samplelist
+ trait_sample_data = trait_ob.data
+ for index, sample in enumerate(trait_samples):
+ if sample in samples:
+ if sample in trait_sample_data:
+ sample_value = trait_sample_data[sample].value
+ this_covar_data.append(sample_value)
+ else:
+ this_covar_data.append("NA")
+
+ for j, item in enumerate(this_covar_data):
+ if j < (len(this_covar_data) - 1):
+ covar_as_string += str(item) + ","
+ else:
+ covar_as_string += str(item)
+
+ covar_as_string += ")"
+
+ col_name = "covar_" + str(i)
+
+ if i < (len(covariate_list) - 1):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ covar_name_string += '"' + col_name + '"'
+
+ cross = add_phenotype(cross, covar_as_string, col_name)
+
+ covar_name_string += ")"
+
+ covars = pull_covar(cross, covar_name_string)
+
+ return cross, covars
+
+def create_marker_covariates(control_marker, cross):
+ ro.globalenv["the_cross"] = cross
+ ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
+ userinputS = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
+ covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
+ ro.r('covnames <- c(' + covariate_names + ')')
+ ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
+ 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
+
+ return ro.r["marker_covars"]
+
def process_pair_scan_results(result):
pair_scan_results = []
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index f03b046e..3006c4ff 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -216,9 +216,9 @@ class RunMapping(object):
#if start_vars['pair_scan'] == "true":
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
- self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
+ self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.samples, self.covariates)
else:
- results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
+ results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.samples, self.covariates)
elif self.mapping_method == "reaper":
if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 0162f858..a2fa37e0 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -107,6 +107,13 @@ $("#remove_covariates").click(function () {
$("input[name=covariates]").val("")
$(".selected_covariates").val("")
});
+$(".select_covariates").click(function () {
+ open_covariate_selection();
+});
+$(".remove_covariates").click(function () {
+ $("input[name=covariates]").val("")
+ $(".selected_covariates").val("")
+});
d3.select("#clear_compare_trait").on("click", (function(_this) {
return function() {
return $('.scatter-matrix-container').remove();
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 6da25a5d..66903c31 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -325,7 +325,23 @@
</label>
</div>
</div>
-
+ <div class="mapping_method_fields form-group">
+ <div class="col-xs-3" style="text-align: right;">
+ <label class="control-label">Covariates</label>
+ <font size="2">Select covariate(s) from a collection</font>
+ </div>
+ <div style="margin-left:20px;" class="col-xs-7">
+ {% if g.user_session.num_collections < 1 %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% else %}
+ <div style="margin-bottom: 10px;">
+ <button type="button" class="btn btn-default select_covariates" style="width: 80px; padding-right: 10px;">Select</button>
+ <button type="button" class="btn btn-default remove_covariates" style="width: 80px;">Remove</button>
+ </div>
+ <textarea rows="3" cols="50" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none; width: 200px;" class="selected_covariates"></textarea>
+ {% endif %}
+ </div>
+ </div>
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 13:40:57 +0000