densityPlot2D

densityPlot2D ¶

densityPlot2D(
    data,
    markerA,
    markerB=None,
    layer=None,
    subset=None,
    imageId="imageid",
    ncols=None,
    cmap="jet",
    figsize=(3, 3),
    hline="auto",
    vline="auto",
    fontSize=None,
    dpi=100,
    xticks=None,
    yticks=None,
    outputDir=None,
    fileName="densityPlot2D.pdf",
    show=True,
    returnData=False,
    returnFig=False,
    transparent=False,
    sdataTable=None,
    **kwargs
)

Two-marker density plots, one panel per marker pair.

Pairs are formed by zipping markerA with markerB. Passing a single list to markerA and leaving markerB as None pairs each marker with the next one, which is a quick way to sweep a panel.

Parameters:

Name	Type	Description	Default
`data`	`(AnnData \| SpatialData \| str, required)`	The cell table. An `AnnData`, a path to an `.h5ad` file, a `SpatialData` object, or a path to a `.zarr` SpatialData store.	required
`markerA`	`(str \| list, required)`	Marker(s) on the x axis.	required
`markerB`	`str \| list`	Marker(s) on the y axis. When `None`, `markerA[1:]` is used, pairing each marker with its successor.	`None`
`layer`	`str`	Which matrix to plot. `None` uses `.X`, `'raw'` uses `.raw.X`, any other string names a key in `.layers`.	`None`
`subset`	`str \| list`	Restrict to these values of `imageId`.	`None`
`imageId`	`str`	Column in `obs` holding image identifiers, used by `subset`.	`'imageid'`
`ncols`	`int`	Panels per row. Defaults to `min(3, number of pairs)`.	`None`
`cmap`	`str`	Matplotlib colormap for the density.	`'jet'`
`figsize`	`tuple`	Size of a single panel in inches.	`(3, 3)`
`hline`	`float`	Horizontal reference line. `'auto'` (the default) draws none.	`'auto'`
`vline`	`float`	Vertical reference line. `'auto'` (the default) draws none.	`'auto'`
`fontSize`	`int`	Axis label font size.	`None`
`xticks`	`list`	Explicit x tick positions.	`None`
`yticks`	`list`	Explicit y tick positions.	`None`
`**kwargs`	`dict`	Passed through to `Axes.hist2d`. `bins` defaults to 100.	`{}`
`outputDir`	`str`	Directory to save the figure in. When `None` nothing is written.	`None`
`fileName`	`str`	File name for the saved figure. The extension decides the format.	`'densityPlot2D.pdf'`
`show`	`bool`	Call `plt.show()` before returning. Set `False` in scripts and notebooks that save rather than display.	`True`
`returnData`	`bool`	Return the `DataFrame` behind the plot instead of drawing it.	`False`
`returnFig`	`bool`	Return `(fig, axes)`. With `returnData` as well, returns `(fig, axes, plotData)`.	`False`
`dpi`	`int`	Resolution of the saved figure.	`100`
`transparent`	`bool`	Save with a transparent background.	`False`
`sdataTable`	`str`	Which `SpatialData` table to read. Ignored for `AnnData` input, and optional when the store has exactly one table.	`None`

Returns:

Name	Type	Description
`result`	`None \| DataFrame \| tuple`	`None` by default; the cell x marker `DataFrame` with `returnData=True`; `(fig, axes)` with `returnFig=True`.

Example

# One biaxial plot with gate lines at the rescaled boundary.
sp.pl.densityPlot2D(
    adata, markerA="CD45", markerB="ECAD", layer="rescaled",
    hline=0.5, vline=0.5,
)

# Several pairs at once.
sp.pl.densityPlot2D(
    adata,
    markerA=["CD45", "CD3", "CD8"],
    markerB=["ECAD", "CD4", "FOXP3"],
    outputDir="figures",
    show=False,
)