stereo.plots.PlotCollection.marker_genes_volcano#
- PlotCollection.marker_genes_volcano(group_name, res_key='marker_genes', hue_order=('down', 'normal', 'up'), colors=('#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.colors (
Optional
[str
]) – the color set.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.