stereo.plots.PlotCollection.marker_genes_heatmap#

PlotCollection.marker_genes_heatmap(res_key, cluster_res_key='cluster', markers_num=5, sort_key='scores', ascend=False, show_labels=True, show_group=True, show_group_txt=True, cluster_colors_array=None, min_value=None, max_value=None, gene_list=None, do_log=True, width=None, height=None)[source]#

Heatmap plot of maker genes.

Parameters:

  • res_key (str) – the result key of marker genes.

  • markers_num (Optional[int]) – top N maker genes.

  • sort_key (Optional[str]) – sorted by which key.

  • ascend (Optional[bool]) – whether to sort by ascending.

  • show_labels (Optional[bool]) – show labels or not.

  • show_group (Optional[bool]) – show group or not.

  • show_group_txt (Optional[bool]) – show group names or not.

  • cluster_colors_array (Optional[bool]) – whether to show color scale.

  • min_value (Optional[int]) – minimum value of scale.

  • max_value (Optional[int]) – maximum value of scale.

  • gene_list (Optional[list]) – gene name list.

  • do_log (Optional[bool]) – perform normalization if log1p before plotting, or not.

  • width (Optional[int]) – the figure width in pixels.

  • height (Optional[int]) – the figure height in pixels.

  • out_path – the path to save the figure.

  • out_dpi – the dpi when the figure is saved.