stereo.plots.PlotCollection.marker_genes_volcano

PlotCollection.marker_genes_volcano(group_name, res_key='marker_genes', hue_order=('down', 'normal', 'up'), palette=('#377EB8', 'grey', '#E41A1C'), alpha=1, dot_size=15, text_genes=None, x_label='log2(fold change)', y_label='-log10(pvalue)', vlines=True, cut_off_pvalue=0.01, cut_off_logFC=1, width=None, height=None, **kwargs)[source]

Volcano plot of maker genes.

Parameters:

  • group_name (str) – the group name.

  • res_key (Optional[str]) – the result key of marker gene.

  • hue_order (Optional[set]) – the classification method.

  • palette (Union[list, tuple, None]) – the color theme, a list of colors whose length is 3, in which, each one respectively specifies the color of ‘down’, ‘normal’ and ‘up’ marker genes.

  • alpha (Optional[int]) – the opacity.

  • dot_size (Optional[int]) – the dot size.

  • text_genes (Optional[list]) – show gene names.

  • x_label (Optional[str]) – the x label.

  • y_label (Optional[str]) – the y label.

  • vlines (Optional[bool]) – plot cutoff line or not.

  • cut_off_pvalue (Optional[float]) – cut off of p-value to define gene type, p-values < cut_off and log2fc > cut_off_logFC

define as up genes, p-values < cut_off and log2fc < -cut_off_logFC define as down genes. :type cut_off_logFC: Optional[int] :param cut_off_logFC: cut off of log2fc to define gene type. :type width: Optional[int] :param width: the figure width in pixels. :type height: Optional[int] :param height: the figure height in pixels. :param out_path: the path to save the figure. :param out_dpi: the dpi when the figure is saved.