emperor.Emperor.color_by¶

Emperor.color_by(category, colors=None, colormap=None, continuous=False)¶

Set the coloring settings for the plot elements

Parameters:

Parameters:	category: str Name of the metadata column. colors: dict or pd.Series, optional Mapping of categories to a CSS color attribute. Defaults to the colors described by `colormap`. colormap: str, optional Name of the colormap to use. Supports continuous and discrete colormaps, see the notes section. Defaults to QIIME’s discrete colorscheme. continuous: bool, optional Whether or not the `category` should be interpreted as numeric.
Returns:	emperor.Emperor Emperor object with updated settings.
Raises:	KeyError If `category` is not part of the metadata. TypeError If `category` is not a string. ValueError If `colors` describes fewer or more categories than the ones present in the `category` column. If `colors` has colors in a non-string format.

category: str

Name of the metadata column.

colors: dict or pd.Series, optional

Mapping of categories to a CSS color attribute. Defaults to the colors described by colormap.

colormap: str, optional

Name of the colormap to use. Supports continuous and discrete colormaps, see the notes section. Defaults to QIIME’s discrete colorscheme.

continuous: bool, optional

Whether or not the category should be interpreted as numeric.

Returns:

emperor.Emperor

Emperor object with updated settings.

Raises:

KeyError

If category is not part of the metadata.

TypeError

If category is not a string.

ValueError

If colors describes fewer or more categories than the ones present in the category column. If colors has colors in a non-string format.

See also

emperor.core.Emperor.visibility_by, emperor.core.Emperor.scale_by, emperor.core.Emperor.opacity_by, emperor.core.Emperor.shape_by, emperor.core.Emperor.set_background_color, emperor.core.Emperor.set_axes

Notes

Valid colormaps are listed below (under the Code column), for examples see [R6] or [R7].

Code	Name	Type
Paired	Paired	Discrete
Accent	Accent	Discrete
Dark2	Dark	Discrete
Set1	Set1	Discrete
Set2	Set2	Discrete
Set3	Set3	Discrete
Pastel1	Pastel1	Discrete
Pastel2	Pastel2	Discrete
Viridis	Viridis	Sequential
Reds	Reds	Sequential
RdPu	Red-Purple	Sequential
Oranges	Oranges	Sequential
OrRd	Orange-Red	Sequential
YlOrBr	Yellow-Orange-Brown	Sequential
YlOrRd	Yellow-Orange-Red	Sequential
YlGn	Yellow-Green	Sequential
YlGnBu	Yellow-Green-Blue	Sequential
Greens	Greens	Sequential
GnBu	Green-Blue	Sequential
Blues	Blues	Sequential
BuGn	Blue-Green	Sequential
BuPu	Blue-Purple	Sequential
Purples	Purples	Sequential
PuRd	Purple-Red	Sequential
PuBuGn	Purple-Blue-Green	Sequential
Greys	Greys	Sequential
Spectral	Spectral	Diverging
RdBu	Red-Blue	Diverging
RdYlGn	Red-Yellow-Green	Diverging
RdYlB	Red-Yellow-Blue	Diverging
RdGy	Red-Grey	Diverging
PiYG	Pink-Yellow-Green	Diverging
BrBG	Brown-Blue-Green	Diverging
PuOr	Purple-Orange	Diverging
PRGn	Purple-Green	Diverging

References

[R6]	(1, 2) https://matplotlib.org/examples/color/colormaps_reference.html

[R7]	(1, 2) http://colorbrewer2.org/