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scirpy.pl.clonotype_modularity

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 (Union[AnnData, MuData, DataHandler]) – AnnData or MuData object that contains AIRR information.

  • ax (default: None) – Add the plot to a predefined Axes object.

  • target_col (default: 'clonotype_modularity') – 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 (Optional[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 (Optional[Sequence[str]] (default: None)) – Explicitly pass a list of clonotypes to label. Overrides labels_quantile_cutoff.

  • label_fontsize (Optional[int] (default: 10)) – Fontsize for the clonotype labels

  • label_fontweight (Union[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 (Optional[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

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