pegasus.qcviolin

pegasus.qcviolin(data, plot_type, min_genes_before_filt=100, n_violin_per_panel=8, panel_size=(6, 4), left=0.2, bottom=0.15, wspace=0.3, hspace=0.35, return_fig=False, dpi=300.0)[source]

Plot quality control statistics (before filtration vs. after filtration) as violin plots. Require statistics such as “n_genes”, “n_counts” and “percent_mito” precomputed.

Parameters
  • data (MultimodalData, UnimodalData, or anndata.AnnData object.) – Single cell expression data.

  • plot_type (str) – Choose from gene, count and mito, which shows number of expressed genes, number of UMIs and percentage of mitochondrial rate.

  • min_genes_before_filt (int, optional, default: 100) – If data loaded are raw data (i.e. min(n_genes) == 0), filter out cell barcodes with less than min_genes_before_filt for better visual effects.

  • n_violin_per_panel (int, optional, default: 8) – Number of violin plots (samples) shown in one panel.

  • panel_size (tuple, optional (default: (6, 4))) – The panel size (width, height) in inches.

  • left (float, optional (default: 0.2)) – This parameter sets the figure’s left margin as a fraction of panel’s width (left * panel_size[0]).

  • bottom (float, optional (default: 0.15)) – This parameter sets the figure’s bottom margin as a fraction of panel’s height (bottom * panel_size[1]).

  • wspace (float, optional (default: 0.4)) – This parameter sets the width between panels and also the figure’s right margin as a fraction of panel’s width (wspace * panel_size[0]).

  • hspace (float, optional (defualt: 0.15)) – This parameter sets the height between panels and also the figure’s top margin as a fraction of panel’s height (hspace * panel_size[1]).

  • 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.

Return type

Optional[Figure]

Returns

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

Examples

>>> pg.qcviolin(data, "mito", dpi = 500)