foldChange

foldChange ¶

foldChange(
    data,
    label="foldchange",
    pVal=0.05,
    nonsigColor="grey",
    subsetXAxis=None,
    subsetYAxis=None,
    cmap="vlag",
    log=True,
    center=0,
    method="heatmap",
    invertAxis=None,
    parallelCoordinatesColor=None,
    fileName="foldchange.pdf",
    outputDir=None,
    saveDir=None,
    show=True,
    returnData=False,
    returnFig=False,
    dpi=300,
    transparent=False,
    sdataTable=None,
    **kwargs
)

Plot cell-type abundance fold changes between groups.

Reads uns[label + "_fc"] (falling back to uns[label]), the matrix that sp.tl.foldChange writes: one row per comparison group, one column per phenotype.

method="heatmap" draws a diverging heatmap centred on center, with the colour limits made symmetric so that equal up- and down-changes read the same. method="parallel_coordinates" draws one line per phenotype across the groups.

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
`label`	`str`	The `label` used when the fold changes were computed. `uns[label + "_fc"]` is preferred, `uns[label]` is the fallback.	`'foldchange'`
`pVal`	`float`	Significance threshold. Accepted for signature compatibility; the current implementation does not mask by p-value.	`0.05`
`nonsigColor`	`str`	Colour for non-significant cells. Accepted for signature compatibility; see `pVal`.	`'grey'`
`subsetXAxis`	`list`	Restrict to these columns (phenotypes).	`None`
`subsetYAxis`	`list`	Restrict to these rows (groups).	`None`
`cmap`	`str`	Matplotlib colormap. `'vlag'` is accepted and mapped to `'coolwarm'`.	`'vlag'`
`log`	`bool`	Plot `log2` of the fold changes. On by default, which is almost always what you want for a ratio.	`True`
`center`	`float`	The value the diverging colormap is centred on. `0` with `log=True`.	`0`
`method`	`str`	`'heatmap'` or `'parallel_coordinates'`.	`'heatmap'`
`invertAxis`	`bool`	Accepted for signature compatibility with scimap; transpose the matrix yourself if you need the other orientation.	`None`
`parallelCoordinatesColor`	`str \| list`	Line colours for `method='parallel_coordinates'`.	`None`
`**kwargs`	`dict`	Extra options. `figsize` sets the figure size in inches; it is scaled from the matrix shape when omitted.	`{}`
`fileName`	`str`	File name for the saved figure. The extension decides the format.	`'foldchange.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 fold-change matrix with `returnData=True`; `(fig, ax)` with `returnFig=True`.

Example

adata = sp.tl.foldChange(adata, fromGroup="control")
sp.pl.foldChange(adata, method="heatmap")
sp.pl.foldChange(adata, method="parallel_coordinates")