plot_qc

scib.preprocessing.plot_qc(adata, color=None, bins=60, legend_loc='right margin', histogram=True, count_threshold=(0, inf), count_filter_threshold=(0, inf), gene_threshold=(0, inf), gene_filter_threshold=(0, inf))

Create QC Plots

Create scatter plot for count depth vs. gene count, and histograms for count depth and gene count. Filtering thresholds are included in all plots for making QC decisions.

Parameters

  • adata – anndata object containing summarised count keys ‘n_counts’ and ‘n_genes’ in adata.obs

  • color – column in adata.obs for the scatter plot

  • bins – number of bins for the histogram

  • legend_loc – location of legend of scatterplot

  • histogram – whether to include histograms

  • count_threshold – tuple of lower and upper count depth thresholds for zooming into histogram plots. By default, this is unbounded and set to the values of count_filter_threshold.

  • count_filter_threshold – tuple of lower and upper count depth thresholds visualised as cutoffs. By default, this is unbounded, so no zoomed in histograms are plotted.

  • gene_threshold – tuple of lower and upper gene count thresholds for zooming into histogram plots. By default, this is unbounded, so no zoomed in histograms are plotted.

  • gene_filter_threshold – tuple of lower and upper gene count thresholds visualised as cutoffs. By default, this is unbounded and set to the values of gene_filter_threshold.