scirpy.pl.clonotype_modularity

scirpy.pl.clonotype_modularity(adata, ax=None, target_col='clonotype_modularity', jitter=0.01, panel_size=(6, 4), base_size=2, size_power=1, show_labels=True, labels_quantile_cutoff=(0.9, 0.9), labels=None, label_fontsize=10, label_fontweight=300, label_fontoutline=0, label_adjusttext=True, show_size_legend=True, legend_width=2, fig_kws=None, airr_mod='airr')

Plots the Clonotype modularity score against the associated log10 p-value.
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Plots the Clonotype modularity score against the associated log10 p-value.

Parameters

adata : AnnData | MuData | DataHandlerUnion[AnnData, MuData, DataHandler]

AnnData or MuData object that contains AIRR information.

ax

Add the plot to a predefined Axes object.

target_col

Column in adata.obs containing the clonotype modularity score and key in adata.uns containing the dictionary with parameters. Will look for p-values or FDRs in adata.obs["{target_col}_pvalue"] or adata.obs["{target_col}_fdr"].

jitter : float (default: 0.01)

Add random jitter along the x axis to avoid overlapping point. Samples from N(0, jitter * (max(arr) - min(arr)))

base_size : float (default: 2)

Size of a point representing 1 cell.

size_power : float | NoneOptional[float] (default: 1)

Point sizes are raised to the power of this value.

show_labels : bool (default: True)

Whether to show text labels for the clonotypes with highest clonotype modularity.

labels_quantile_cutoff : Tuple[float, float] (default: (0.9, 0.9))

Label clonotypes with exceeding the given quantile cutoff. Only unique values are considered for calculating the quantiles (avoiding thousands of singleton clonotypes with modularity 0). The cutoff is specified as a tuple (cutoff_for_modularity, cutoff_for_pvalue).

labels : Sequence[str] | NoneOptional[Sequence[str]] (default: None)

Explicitly pass a list of clonotypes to label. Overrides labels_quantile_cutoff.

label_fontsize : int | NoneOptional[int] (default: 10)

Fontsize for the clonotype labels

label_fontweight : str | floatUnion[str, float] (default: 300)

Fontweight for the clonotype labels

label_fontoutline : int (default: 0)

Size of the fontoutline added to the clonotype labels. Set to None to disable.

label_adjusttext : bool (default: True)

Whether to “repel” labels such that they don’t overlap using the adjustText library. This option significantly increases the runtime.

show_size_legend : bool (default: True)

Whether to show a legend for dot sizes on the right margin

legend_width : float (default: 2)

Width of the legend column in inches. Only applies if show_size_legend is True

fig_kws : dict | NoneOptional[dict] (default: None)

Parameters passed to the matplotlib.pyplot.figure() call if no ax is specified.

airr_mod : str (default: 'airr')

Name of the modality with AIRR information is stored in the MuData object. if an AnnData object is passed to the function, this parameter is ignored.

Returns

A list of axis objects