GSForge.plots.abstract_plot_models module

class GSForge.plots.abstract_plot_models.AbstractPlottingOperation(*args, **params)

Bases: param.parameterized.ParameterizedFunction

apply_default_opts = param.Boolean(readonly=False)

Whether to apply the default styling based on the current backend.

plot_options = param.Parameter(readonly=False)

User supplied options to the plotting functions. If provided (and is not None), these will take precedence over a functions built-in defaults.

apply_default_opts = True
plot_options = None
static bokeh_opts()
static matplotlib_opts()
get_default_options()

Apply default styling options by default.

get_param_process_overlap_kwargs(process) → dict

Gets overlapping kwargs of the given process and parameters of a Parameterized class, and returns them as a dictionary.

name = 'AbstractPlottingOperation'
class GSForge.plots.abstract_plot_models.InterfacePlottingBase(**kwargs)

Bases: GSForge.models._Interface.CallableInterface, GSForge.plots.abstract_plot_models.AbstractPlottingOperation

This abstract base class should be used for plotting operations that act upon a GSForge interface object, and which directly return a plot.

Parameters inherited from:

GSForge.plots.abstract_plot_models.AbstractPlottingOperation: apply_default_opts, plot_options

GSForge.models._Interface.Interface: gem, gene_set_collection, selected_gene_sets, selected_genes, gene_set_mode, sample_subset, count_variable, annotation_variables, count_mask, annotation_mask, count_transform

name = 'InterfacePlottingBase'
class GSForge.plots.abstract_plot_models.ResultPlottingOperation(*args, **params)

Bases: GSForge.plots.abstract_plot_models.AbstractPlottingOperation

Parameters inherited from:

source = param.Parameter(readonly=False)

source = None
DGE_DEFAULT_KWARGS = {'log_fold_change_var': ['logFC', 'log2FoldChange'], 'mean_value_var': ['baseMean', 'logCPM'], 'p_value_var': ['pvalue', 'PValue']}
classmethod infer_kwarg_defaults_from_data(source: xarray.core.dataset.Dataset, function) → dict

Try to infer variable names for plotting functions. e.g. Try to find what the ‘p-value’ column.

name = 'ResultPlottingOperation'