distPlot

distPlot ¶

distPlot(
    data,
    layer=None,
    markers=None,
    subset=None,
    imageId="imageid",
    vline=None,
    plotGrid=True,
    ncols=None,
    color=None,
    xticks=None,
    figsize=(5, 5),
    fontSize=None,
    dpi=200,
    outputDir=None,
    fileName="scimapDistPlot.png",
    show=True,
    returnData=False,
    returnFig=False,
    transparent=False,
    sdataTable=None,
    **kwargs
)

Per-marker intensity histograms in a grid.

One histogram per marker, drawn from whichever matrix layer selects. Pass vline to draw a candidate gate across every panel — on rescaled data that is usually 0.5.

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
`layer`	`str`	Which matrix to plot. `None` uses `.X`, `'raw'` uses `.raw.X`, any other string names a key in `.layers`.	`None`
`markers`	`list`	Markers to plot. All of them when `None`.	`None`
`subset`	`str \| list`	Restrict to these values of `imageId`.	`None`
`imageId`	`str`	Column in `obs` holding image identifiers, used by `subset`.	`'imageid'`
`vline`	`float`	Draw a vertical reference line at this value in every panel.	`None`
`plotGrid`	`bool`	Draw a faint grid behind each histogram.	`True`
`ncols`	`int`	Panels per row. Defaults to `min(4, number of markers)`.	`None`
`color`	`str`	Bar colour.	`None`
`xticks`	`list`	Explicit x tick positions.	`None`
`figsize`	`tuple`	Size of a single panel in inches; the figure is scaled by the grid.	`(5, 5)`
`fontSize`	`int`	Panel title font size.	`None`
`**kwargs`	`dict`	Passed through to `Axes.hist`. `bins` defaults to 50.	`{}`
`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.	`'scimapDistPlot.png'`
`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.	`200`
`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

# Every marker, with the rescaled 0.5 boundary marked.
sp.pl.distPlot(adata, layer="rescaled", vline=0.5)

# Two markers in one image, saved.
sp.pl.distPlot(
    adata,
    markers=["CD45", "ECAD"],
    subset="sample_1",
    outputDir="figures",
    fileName="gates.png",
    show=False,
)