Mysql Models¶

class NetExplorer.models.mysql_models.CellPlotPosition(*args, **kwargs)¶

Table with Cell position in a 2-dimensional space, usually computed with t-SNE.

experiment¶: Foreign Key to Experiment.

sample¶: Foreign Key to Sample.

dataset¶: Foreign Key to Dataset.

x_position¶: Float with x-axis coordinate.

y_position¶: Float with y-axis coordinate.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

sample

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

sample_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

x_position: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

y_position: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class NetExplorer.models.mysql_models.ClusterMarkers(*args, **kwargs)¶

Class for cluster marker genes.

experiment¶: Foreign Key to Experiment.

dataset¶: Foreign Key to Dataset.

condition¶: Foreign Key to Condition.

gene_symbol¶: String with gene symbol.

auc¶: Area under the curve of the marker used as a classifier.

avg_diff¶: Average difference in expression of the marker between this condition and all the others.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

auc: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

avg_diff: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

condition

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

condition_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

gene_symbol: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

class NetExplorer.models.mysql_models.Condition(*args, **kwargs)¶

Table with PlanExp experiment conditions. Technical conditions, Experimental conditions, Clusters, etc. will be stored here.

name¶: Name of condition.

experiment¶: Foreign Key to Experiment.

cond_type¶: Foreign Key to ConditionType.

defines_cell_type¶: Boolean field indicating if condition defines cell types (e.g.: cluster).

cell_type¶: If defines_cell_type is True, then cell_type stores the name of the cell type this condition defines.

description¶: Description of the Condition.

max_expression¶: Maximum expression value in this condition (defaults to None).

min_expression¶: Minimum expression value in this condition (default to 0).

exception DoesNotExist¶

exception MultipleObjectsReturned¶

_Condition__get_max_expression()¶: Gets max expression of samples in this particular condition. Assigns it to self.max_expression and returns it.

cell_type: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

clustermarkers_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

cond_type

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

cond_type_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

condition1_expressionrelative_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

condition1_expressionrelative_setsubcondition¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

defines_cell_type: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

description: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

expressioncondition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

get_color(dataset, value, profile='red', max_v=None)¶

Returns expression color for a given expression value. Will use one of the saved color profiles ‘red’, ‘green’ or ‘blue’.

If max_v is provided, the color will be determined using a scale from 0 to max_v. Otherwise, max_v will be computed as the maximum expression value for a particular experiment + condition.

get_color_legend(profile='red', units=None)¶: Returns html of color gradient generated for expression in Condition

classmethod get_samples_per_condition(experiment, ctype)¶

Method for getting the number of samples per condition of ctype.

Parameters

experiment (str) – Experiment name.
ctype (str) – Condition type.

Returns

Dictionary with conditions and samples mapping.: Keys are condition ids (int) values are number of samples (int) in that condition.

Return type

sc_dict (dict)

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

max_expression = None

min_expression = 0

name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

samplecondition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class NetExplorer.models.mysql_models.ConditionType(*args, **kwargs)¶

Types of conditions for a PlanExp experiment. 1 Batch (technical condition). 2 Experimental condition. 3 Cluster.

name¶: Condition Type name.

description¶: Description for condition type.

is_interaction¶: Bool to define if it results from an interaction of other condition types.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

condition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

description: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

expressionrelative_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

is_interaction: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

class NetExplorer.models.mysql_models.Dataset(*args, **kwargs)¶

Model that describes the table for storing information about the transcriptome Datasets available in PlanExp and PlanNET.

name¶: Name of the dataset.

year¶: Year of publication (if available).

citation¶: Citation string to be shown on the website.

url¶: Url to the publication.

n_contigs¶: Number of contigs (transcripts) in this dataset.

n_ints¶: Number of predicted interactions for this dataset.

identifier_regex¶: Regular expression of the identifiers used for this dataset.

public¶: Boolean to define if it is a public dataset (True) or private (False).

exception DoesNotExist¶

exception MultipleObjectsReturned¶

cellplotposition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

citation: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

clustermarkers_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

experimentdataset_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

expressionabsolute_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

expressionrelative_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

classmethod get_allowed_datasets(user)¶

Classmethod that returns QuerySet of allowed datasets for a given user.

Parameters

user (User) – User object.

Returns

List of Dataset objects sorted by year: to which user has permissions to.

Return type

list of Dataset

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

identifier_regex: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

is_symbol_valid(symbol)¶

Checks if a given symbol belongs to Dataset based on the symbol naming convention.

Parameters

symbol (str) – String of an identifier to check if it matches the regex for this dataset.

Returns

True if symbol belongs to this Dataset,: otherwise False.

Return type

bool

n_contigs: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

n_ints: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

public: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

regulatorylinks_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

url: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

userdatasetpermission_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

year: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class NetExplorer.models.mysql_models.Experiment(*args, **kwargs)¶

Table with RNA-seq and scRNA-seq Experiment information.

name¶: Name of the experiment.

description¶: Description of the experiment.

citation¶: Citation string of experiment publication.

url¶: Url of the publication.

exp_type¶: Foreign Key to the corresponding ExperimentType.

public¶: Boolean to define if it is a public experiment (True) or private (False).

exception DoesNotExist¶

exception MultipleObjectsReturned¶

cellplotposition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

citation: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

clustermarkers_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

condition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

description: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

exp_type

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

exp_type_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experimentdataset_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

experimentgene_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

expressionabsolute_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

expressioncondition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

expressionrelative_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

classmethod get_allowed_experiments(user)¶

Returns QuerySet of allowed experiments for a given user.

Parameters

user (User) – User for which to retrieve allowed experiments.

Returns

QuerySet of allowed experiments to which user has: permission to.

Return type

QuerySet

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

is_one_sample(ctype=None, conditions=None)¶

Checks if there is only one sample per condition in experiment.

Parameters

ctype (str) – ConditionType name.
conditions (list of Condition) – List of conditions for Experiment.

Returns

True if experiment has only one sample per condition. False otherwise.

Return type

bool

Raises

ValueError – If neither ‘ctype’ nor ‘conditions’ is provided.

name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

public: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

regulatorylinks_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

sample_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

samplecondition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

to_json()¶

Returns json string with info about experiment.

Returns

JSON string of serialized Experiment. Contains:

’name’
’description’
’citation’
’url’
’type’

Return type

str

url: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

userexperimentpermission_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class NetExplorer.models.mysql_models.ExperimentDataset(*args, **kwargs)¶

Table with Datasets available for a particular experiment.

dataset¶: Foreign Key to Dataset.

experiment¶: Foreign Key to Experiment.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

class NetExplorer.models.mysql_models.ExperimentGene(*args, **kwargs)¶

Table with genes that appear in a particular experiment. Useful for deciding if a gene has expression == 0.

If gene is in ExperimentGene but not in ExpressionAbsolute: expression == 0. If gene is not in ExperimentGene: expression == “NA”

experiment¶: Foreign Key to Experiment.

gene_symbol¶: String with gene symbol.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

gene_symbol: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

class NetExplorer.models.mysql_models.ExperimentType(*args, **kwargs)¶

Table with experiment types in PlanExp.

exp_type¶: Name of the experiment type.

description¶: Description of the experiment type.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

description: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

exp_type: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

class NetExplorer.models.mysql_models.ExpressionAbsolute(*args, **kwargs)¶

Stores expression for a particular gene in a particular sample. Only stores NON-ZERO values.

experiment¶: Foreign Key to Experiment to which sample belongs to.

sample¶: Foreign Key to Sample.

dataset¶: Foreign Key to Dataset to which gene_symbol belongs to.

gene_symbol¶: String with gene symbol.

expression_value¶: Float with the expression value for gene_symbol in sample.

units¶: Units in which expression_value are stored (usually logCPM).

exception DoesNotExist¶

exception MultipleObjectsReturned¶

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

expression_value: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

gene_symbol: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

classmethod get_mean_expression(experiment, dataset, conditions, genes)¶

Returns mean gene expression for samples with expression > 0 for all provided genes.

Example

For genes A and B, will get a value for each cell in experiment where both genes are expressed > 0. Each value will be the mean expression (A + B) / 2 for each sample.

Parameters

experiment (str) – Experiment in PlanExp.
dataset (str) – Dataset in PlanExp.
conditions (list of Condition) – Conditions (previously sorted) to use for the plot.
genes (list of str) – Genes to plot. Can be empty depending on the plot.

Returns

Dictionary with mean expession for condition.: Key is sample name (str), value is mean expression (float) for each gene in genes. Only samples with expression for all genes in genes.

Return type

dict

classmethod get_sample_expression(experiment, dataset, conditions, genes, only_expressed=False)¶

Method for getting gene expression in all samples.

Parameters

experiment (str) – Experiment in PlanExp.
dataset (str) – Dataset in PlanExp.
conditions (list of Condition) – Conditions (previously sorted) to use for the plot.
genes (list of str) – Genes to plot. Can be empty depending on the plot.
only_expressed (bool) – Flag, return only expression for samples with expression > 0?

Returns

Two dictionaries.

1st: Key is gene symbol (str), value is vector of expression in each sample (list of float), sorted by condition.

2nd: Key is gene_symbol (str), value is vector with conditions for each sample (list of int), same order as list in 1st dictionary.
dict1 = {
    'gene1': [ float, float, float, ...],
    ...
}
dict2 = {
    'gene1': [ int, int, int, ...],
    ...
}

Return type

(dict, dict)

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

sample

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

sample_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

units: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class NetExplorer.models.mysql_models.ExpressionCondition(*args, **kwargs)¶

Table that stores the sum of expression values in a particular condition. Note that we store the sum, and not the mean, because the 0 values of expression are not stored in ExpressionAbsolute, and thus can’t be computed without taking into account the number of samples in each condition separately.

experiment¶: Foreign Key to Experiment.

gene_symbol¶: Gene symbol.

condition¶: Foreign Key to Condition.

sum_expression¶: The sum of expression values for gene_symbol in all samples that belong to condition.

To create it:

CREATE TABLE NetExplorer_expressioncondition
SELECT `NetExplorer_expressionabsolute`.`experiment_id`,
    `NetExplorer_samplecondition`.`condition_id`,
    `NetExplorer_expressionabsolute`.`gene_symbol`,
        SUM(`NetExplorer_expressionabsolute`.`expression_value`) AS sum_expression
FROM  `NetExplorer_expressionabsolute`
INNER JOIN NetExplorer_samplecondition ON NetExplorer_expressionabsolute.sample_id = NetExplorer_samplecondition.sample_id
GROUP BY `NetExplorer_samplecondition`.`condition_id`,
        `NetExplorer_expressionabsolute`.`gene_symbol`,
        `NetExplorer_expressionabsolute`.`experiment_id`;

exception DoesNotExist¶

exception MultipleObjectsReturned¶

condition

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

condition_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

gene_symbol: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

classmethod get_condition_expression(experiment, dataset, conditions, ctype, genes)¶

Method for getting gene expression in a set of conditions.

Parameters

experiment (str) – Experiment in PlanExp.
dataset (str) – Dataset in PlanExp.
conditions (list of Condition) – Conditions (previously sorted) to use for the plot.
genes (list of str) – Genes to plot. Can be empty depending on the plot.

Returns

Dictionary with expression for each condition.: Key is gene symbol (str), value is vector of expression in each condition (list of float), in the same order as conditions.

Return type

dict

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

sum_expression: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class NetExplorer.models.mysql_models.ExpressionRelative(*args, **kwargs)¶

Table for storing comparisons of expression between two conditions. Only stores significant results.

experiment¶: Foreign Key to Experiment.

condition1¶: Foreign Key to Condition.

condition2¶: Foreign Key to Condition.

cond_type¶: Foreign Key to ConditionType.

dataset¶: Foreign Key to Dataset.

gene_symbol¶: String with gene symbol.

fold_change¶: Float with log2(Fold Change).

pvalue¶: Float with adjusted p-value.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

cond_type

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

cond_type_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

condition1

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

condition1_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

condition2

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

condition2_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

fold_change: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

gene_symbol: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

pvalue: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class NetExplorer.models.mysql_models.RegulatoryLinks(*args, **kwargs)¶

Class for regulatory links predicted for a SingleCell Experiment.

experiment¶: Foreign Key to Experiment.

dataset¶: Foreign Key to Dataset.

group¶: Integer from 1 to 10 that indicates to which group of links it belongs to, ordered from best (1) to worse (10). Each group has 100 links.

regulator¶: Gene symbol of the regulator gene.

target¶: Gene symbol of the target gene.

source¶: String indicating if the regulator was selected by PFAM domain or by GO term.

score¶: Score of the regulatory link as reported by GENIE3.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

group: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

regulator: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

score: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

source: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

target: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class NetExplorer.models.mysql_models.Sample(*args, **kwargs)¶

Table for storing samples.

experiment¶: Foreign Key to experiment to which sample belongs to.

sample_name¶: Sample name.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

cellplotposition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

expressionabsolute_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

sample_name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

samplecondition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class NetExplorer.models.mysql_models.SampleCondition(*args, **kwargs)¶

Table with Conditions to which each sample belongs.

experiment¶: Foreign Key to Experiment.

sample¶: Foreign Key to Sample.

condition¶: Foreign Key to Condition.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

condition

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

condition_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

sample

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

sample_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class NetExplorer.models.mysql_models.UserDatasetPermission(*args, **kwargs)¶

Table with user permissions to Datasets.

user¶: ForeignKey to User.

dataset¶: ForeignKey to Dataset.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

user

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

user_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class NetExplorer.models.mysql_models.UserExperimentPermission(*args, **kwargs)¶

Table with user permissions to experiments in PlanExp.

user¶: Foreign Key to User.

experiment¶: Foreign Key to Experiment.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

user

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

user_id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.