pegasus.plot_infercnv

pegasus.plot_infercnv(data, groupby, ref_cat=None, tumor_cat=None, rep='cnv', panel_size=(16, 10), cmap='bwr', legend_fontsize=10.0, show_groupby_border=False, return_fig=False, dpi=300.0, output_file=None, **kwargs)[source]

Generate InferCNV plot based on the results calculate by calc_infercnv function.

Parameters

  • data (MultimodalData or UnimodalData object) – Single-cell data matrix.

  • groupby (str) – Specify the key for grouping cells in the heatmap. Must exist in data.obs.

  • ref_cat (str, optional, default: None) – Specify the categories in data.obs[groupby] that is treated as reference (i.e. non-malignant cell groups). If None, which is the default, treat all cell groups as tumor, and only show one heatmap for all groups.

  • tumor_cat (str, optional, default: None) – Specify the categories in data.obs[groupby] that is treated as tumor (i.e. malignant cell groups). If None, which is the default, and if ref_cat is not None, then treat all cell groups not in ref_cat as tumor groups. In this case, there will be 2 heatmaps: one for reference, one for tumor. Otherwise, if there are still cell groups not in ref_cat or tumor_cat, then there will be 3 heatmaps: one for reference on top, one for tumor on bottom, and one for the rest groups in middle.

  • rep (str, optional, default: cnv) – Specify the key for CNV results stored in data. By default, use the default result key of calc_infercnv function.

  • panel_size ((int, int), optional, default: (16, 10)) – Specify the figure size in (width, height) format.

  • cmap (str, optional, default: bwr) – Color map for plotting heatmap. Available options are in Matplotlib colormaps manual.

  • legend_fontsize (float, optional, default: 10.0) – Font size of legend, as well as chromosome names shown at the bottom of plot.

  • show_groupby_border (bool, optional, default: False) – If show cell group borders as horizontal lines in each heatmap. Do not show them by default.

  • return_fig (bool, optional, default: False) – Return a Figure object if True; return None otherwise.

  • dpi (float, optional, default: 300.0) – The resolution in dots per inch.

  • output_file (str, optional, default: None) – The filename when saving the plot as file. If None, which is the default, do not save to file.

Return type

Optional[Figure]

Returns

  • Figure object – A matplotlib.figure.Figure object containing the dot plot if return_fig == True.

Examples

>>> plot_infercnv(data, groupby="anno", ref_cat=["Macrophage", "T", "B", "Plasma"])