Plots¶

class NetExplorer.models.plots.BarPlot¶

Class for Plotly bar plots where each bar (group) consists of only one value. Inherits from GenExpPlot.

plot()¶

Converts plot to a JSON string ready to be drawn by Plotly.js.

Returns: JSON string with plot data for Plotly.js.
Return type: str

class NetExplorer.models.plots.GeneExpPlot¶

Parent class for Plotly barplots and violins.

traces¶

List of plotly traces that define the data to be plotted.

Type: list of PlotlyTrace

title¶

Title for plot.

Type: str

xlab¶

Label for plot x-axis.

Type: str

ylab¶

Label for plot y-axis.

Type: str

trace_names¶

Name for traces, if any.

Type: list of str

is_empty()¶

Checks if plot is empty by looking at its traces.

Returns: True if empty, False otherwise.
Return type: bool

plot()¶: Method to be provided by child classes to convert plot to JSON string for plotting.

class NetExplorer.models.plots.HeatmapPlot¶

Class for plotly Heatmaps. They are not GeneExpPlot because they function very differently.

x¶

x-values for data (condition names).

Type: list of str

y¶

y-values for data (gene names).

Type: list of str

z¶

z-values for data (expression that will be mapped to color). Each element of z corresponds to a list with expression values for one gene. z is a 2-D matrix where rows are genes (same order as y) and columns are conditions (same order as x).

Type: list of list

type¶

Defines type for Plotly (“heatmap”).

Type: str

Warning

add_gene and add_gene_expression should be used syncronously. Each time a gene is added, all gene_expressions will be added for THAT gene. Those should be added in the same order as the provided conditions in the add_condition call previously. See the example for more information.

Example

# Data to be added
genes = ["A", "B"]
expressions = [
    [2.5, 3.5, 4.5], # for A
    [1, 3, 1] # for B
]
conditions = ["c1", "c2", "c3"]

# Initialize the plot
the_plot = HeatMapPlot()
theplot.add_conditions(conditions)

# Add genes and expression
for gene, expression in zip(genes, expressions):
    theplot.add_gene(gene)
    theplot.add_gene_expression(expression)

add_conditions(conditions)¶

Adds conditions to x-axis.

Parameters: conditions (list of Condition or str) – Conditions to be added.

add_gene(gene_symbol)¶

Adds gene symbol to y-axis.

Parameters: gene_symbol (str) – Gene symbol to be added to y-axis.

add_gene_expression(expression)¶

Adds gene expression to z-axis.

Parameters: expression (float) – Expression value to be added to the LAST gene.

is_empty()¶

Checks if plot is empty by looking at its traces.

Returns: True if empty, False otherwise.
Return type: bool

plot()¶

Converts plot to a JSON string ready to be drawn by Plotly.js.

Returns: JSON string with plot data for Plotly.js.
Return type: str

class NetExplorer.models.plots.LinePlot¶

Class for Plotly linecharts. Inherits from GenExpPlot.

type¶

Type for Plotlyjs (scattergl).

Type: str

plot()¶

Converts plot to a JSON string ready to be drawn by Plotly.js.

Returns: JSON string with plot data for Plotly.js.
Return type: str

class NetExplorer.models.plots.PlotCreator¶

Class that handles the creation of plots for PlanExp.

_PlotCreator__create_bar(**kwargs)¶

Creates a bar plot.

Parameters: **kwargs – Arbitrary keyword arguments passed from create_plot.
Returns: Bar plot instance.
Return type: BarPlot

_PlotCreator__create_coexpression(**kwargs)¶

Creates a co-expression plot, a plot where x and y axis are expression values for two genes, and each point is a cell.

Parameters: **kwargs – Arbitrary keyword arguments passed from create_plot.
Returns: ScatterPlot plot instance with co-expression plot.
Return type: ScatterPlot

_PlotCreator__create_heatmap(**kwargs)¶

Creates a heatmap plot.

Parameters: **kwargs – Arbitrary keyword arguments passed from create_plot.
Returns: Heatmap plot instance.
Return type: HeatmapPlot

_PlotCreator__create_linechart(**kwargs)¶

Creates a linechart plot.

Parameters: **kwargs – Arbitrary keyword arguments passed from create_plot.
Returns: Line chart plot instance.
Return type: LinePlot

_PlotCreator__create_tsne(**kwargs)¶

Creates either a simple t-SNE (zero or one gene) or a multiple t-SNE (>1 gene).

Parameters: **kwargs – Arbitrary keyword arguments passed from create_plot.
Returns: Scatter plot t-SNE visualization.
Return type: ScatterPlot

_PlotCreator__create_tsne_multiple(cell_positions, sample_names, sample_condition, sample_mean_expression)¶

Creates a t-SNE plot withmore than one gene expression mapped onto it.

Parameters

genes (list of str) – List of gene symbols.
cell_positions (dict) – Dictionary with cell positions in t-SNE space. Key is cell/sample name, value is tuple with (x, y) positions (float, float).
sample_names (list of str) – List of sample names.
sample_condition (dict) – Dictionary with sample-condition relationships. Key is cell/sample name, value is condition identifier (int).
sample_mean_expression (dict) – Dictionary with mean expession for condition. Key is sample name (str), value is mean expression (float) for each gene in genes in that cell.

Returns

ScatterPlot plot instance.

Return type

ScatterPlot

_PlotCreator__create_tsne_simple(genes, cell_positions, sample_names, sample_condition, sample_expression)¶

Creates a t-SNE plot with one (or none) gene expression mapped onto it.

Parameters

genes (list of str) – List of gene symbols.
cell_positions (dict) – Dictionary with cell positions in t-SNE space. Key is cell/sample name, value is tuple with (x, y) positions (float, float).
sample_names (list of str) – List of sample names.
sample_condition (dict) – Dictionary with sample-condition relationships. Key is cell/sample name, value is condition identifier (int).
sample_expression (dict) – Key is gene symbol (str), value is vector of expression in each sample (list of float), sorted by condition.

Warning

sample_expression values have to be in the same order as sample_names! We sort them by sample identifier using order(‘sample’) in Django models.

Returns: ScatterPlot plot instance.
Return type: ScatterPlot

_PlotCreator__create_violin(**kwargs)¶

Creates a violin plot.

Parameters: **kwargs – Arbitrary keyword arguments passed from create_plot.
Returns: Violin plot instance.
Return type: ViolinPlot

create_plot(plot_name, **kwargs)¶

Method for creating plots.

Parameters

plot_name (str) – Name of the plot. Can be (violin, tsne, coexpression, bar, heatmap or line)
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.
ctype (str) – Condition type of conditions.
only_toggle (bool, optional) – Plot only samples with expression > 0. Used only for plot violin.

Returns

Can be of subclass (ViolinPlot, ScatterPlot,: BarPlot, HeatmapPlot, or LinePlot).

Return type

plot (GeneExpPlot)

class NetExplorer.models.plots.PlotlyTrace(name)¶

Class for plotly traces.

name¶

Type: str

class NetExplorer.models.plots.ScatterPlot¶

Class for scatter plots. Inherits from GenExpPlot.

type¶

Type for Plotlyjs (scattergl).

Type: str

cmax¶

Maximum value to compute color gradient. Defaults to None.

Type: float

cmin¶

Minimum value to compute color gradient. Defaults to 0.

Type: int

compute_color_limits()¶

Computes color limits according to stored trace values and fills cmax attribute.

Raises: EmptyPlotError – raised when no values are found in traces.

plot()¶

Converts plot to a JSON string ready to be drawn by Plotly.js.

Returns: JSON string with plot data for Plotly.js.
Return type: str

class NetExplorer.models.plots.ViolinPlot¶

Class for Plotly violinplots. Each violin (group) is made of multiple values. Inherits from GenExpPlot.

jitter_and_round(values, jitter=0.01)¶

Jitters the y-values of the Violin plot so that Plotly can plot them because Plotly.js is buggy as hell, and if the standard deviation is equal to zero it will REFUSE to plot the violin.

Parameters

values (list of float) – Values to be jittered.
jitter (float) – How much to jitter the y-values.

plot()¶

Converts plot to a JSON string ready to be drawn by Plotly.js.

Returns: JSON string with plot data for Plotly.js.
Return type: str

class NetExplorer.models.plots.VolcanoPlot¶

Class for Plotly volcano scatterplots. Legacy code that should be converted to ScatterPlot at some point.

var data = [

{
z: [[1, 20, 30, 50, 1], [20, 1, 60, 80, 30], [30, 60, 1, -10, 20]], x: [‘Monday’, ‘Tuesday’, ‘Wednesday’, ‘Thursday’, ‘Friday’], y: [‘Morning’, ‘Afternoon’, ‘Evening’], type: ‘heatmap’

} ];

Plotly.newPlot(‘myDiv’, data);

add_color_to_trace(trace_name, colors)¶

add_name(trace_name, name)¶

add_trace(name)¶

add_units(axis, units)¶

Adds units to one axis of the plot.

Parameters

axis – string cointaining ‘x’ or ‘y’.
units – string for units.

Returns

nothing

add_x(trace_name, x)¶

add_y(trace_name, y)¶

plot()¶

set_limits(axis, start, end)¶