markerCorrelation

markerCorrelation ¶

markerCorrelation(
    data,
    layer="log",
    subsetMarkers=None,
    orderRow=None,
    orderColumn=None,
    clusterRows=True,
    clusterColumns=True,
    cmap="vlag",
    figsize=None,
    overlayValues=False,
    fontSize=10,
    fontColor="black",
    fileName="markerCorrelation.pdf",
    outputDir=None,
    saveDir=None,
    show=True,
    returnData=False,
    returnFig=False,
    dpi=300,
    transparent=False,
    sdataTable=None,
    **kwargs
)

Marker-by-marker Pearson correlation across all cells, as a heatmap.

Highly correlated markers usually mean either real co-expression or a staining artefact worth investigating before phenotyping.

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 correlate. Defaults to `'log'`; `None` uses `.X`, `'raw'` uses `.raw.X`, any other string names a key in `.layers`.	`'log'`
`subsetMarkers`	`list`	Restrict to these markers.	`None`
`orderRow`	`list`	Explicit row order.	`None`
`orderColumn`	`list`	Explicit column order.	`None`
`clusterRows`	`bool`	Accepted for signature compatibility with scimap; the current implementation does not reorder rows. Use `orderRow` instead.	`True`
`clusterColumns`	`bool`	Accepted for signature compatibility with scimap; the current implementation does not reorder columns. Use `orderColumn` instead.	`True`
`cmap`	`str`	Matplotlib colormap. `'vlag'` is accepted and mapped to `'coolwarm'`.	`'vlag'`
`figsize`	`tuple`	Figure size in inches. Scaled from the matrix shape when `None`.	`None`
`overlayValues`	`bool`	Print the correlation coefficient inside each cell.	`False`
`fontSize`	`int`	Tick label font size.	`10`
`fontColor`	`str`	Accepted for signature compatibility with scimap; overlaid values are drawn in the default text colour.	`'black'`
`fileName`	`str`	File name for the saved figure. The extension decides the format.	`'markerCorrelation.pdf'`
`outputDir`	`str`	Directory to save the figure in. When `None` nothing is written.	`None`
`saveDir`	`str`	Deprecated alias for `outputDir`, kept for scripts carried over from scimap. `outputDir` wins when both are given.	`None`
`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.	`300`
`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 marker x marker correlation matrix with `returnData=True`; `(fig, ax)` with `returnFig=True`.

Example

sp.pl.markerCorrelation(adata, layer="log", overlayValues=True)

corr = sp.pl.markerCorrelation(
    adata, subsetMarkers=["CD45", "CD3", "CD8", "FOXP3"], returnData=True
)