mcbrowse.figures.gene_gene¶

A gene-gene scatter figure.

This figure is the workhorse of annotating metacells with “cell types”. It shows which combinations of the two genes exist, gradients between different states, and how all these match the current type annotation.

class mcbrowse.figures.gene_gene.GeneGeneFilter(x_gene_name: str, y_gene_name: str, metacell_value: str = 'type', metacell_tooltip: Union[None, str, Tuple[str, str], Sequence[Union[str, Tuple[str, str]]], Callable[[DafReader], Sequence[Optional[str]]]] = None)[source]¶

Bases: FigureFilter[GeneGeneData]

Collect the data for a gene-gene figure.

x_gene_name: str¶

The name of the gene to use for the X axis.

This is stored in a column called x_gene_fractions in the collected data frame.

y_gene_name: str¶

The name of the gene to use for the Y axis.

This is stored in a column called y_gene_fractions in the collected data frame.

metacell_value: str = 'type'¶

The value to assign a value to each metacell (for coloring).

This is stored in a column called metacell_value in the collected data frame. It should be the name of some 1D data associated with each metacell in the daf data, that is, type will be used to access the metacell;type 1D data.

Converting the values to colors is done in the GeneGeneVeneer.

metacell_tooltip: Union[None, str, Tuple[str, str], Sequence[Union[str, Tuple[str, str]]], Callable[[daf.access.readers.DafReader], Sequence[Optional[str]]]] = None¶: How to compute a tooltip for each metacell.

collect(data: DafReader) → GeneGeneData[source]¶: Collect the matching FigureData out of the data.

mcbrowse.figures.gene_gene.GeneGeneData¶

Contain the data for a gene-gene figure.

It will contain the columns: x_gene_fraction, y_gene_fraction, metacell_value and metacell_tooltip.

alias of TidyFigureData

class mcbrowse.figures.gene_gene.GeneGeneVeneer(*args, **kwds)[source]¶

Bases: FigureVeneer[GeneGeneData]

Control the appearance of a gene-gene figure.

figure: Optional[mcbrowse.figures.interface.FigureVeneer] = None¶: The overall figure parameters.

x_axis: Optional[mcbrowse.common.veneers.ContinuousAxisVeneer] = None¶: Control the X axis.

y_axis: Optional[mcbrowse.common.veneers.ContinuousAxisVeneer] = None¶: Control the Y axis.

points: Optional[mcbrowse.common.veneers.PointsVeneer] = None¶: Control the point appearance.

highlighted_points: Optional[mcbrowse.common.veneers.PointsVeneer] = None¶: Control the appearance of highlighted points.

tooltips: Optional[mcbrowse.common.veneers.TooltipsVeneer]¶: Control the appearance of the tooltips.

colors: Union[mcbrowse.common.veneers.DiscreteAxisVeneer, mcbrowse.common.veneers.ContinuousColorScale]¶: How to color the metacells.

plot(data: GeneGeneData) → BaseFigure[source]¶: Generate the plotly figure using the specified data.