API Reference

Cellestial is built on top of Lets-Plot. For further customization options, functionalities, utilities and many more please refer to Lets-Plot API.

Base

plot	Base plot (for plots without data wrangling).

Basic

bar	Bar Plot.
scatter	Scatter Plot.

QC

ridge	Ridge Plot.
ridges	Ridge Plot.
highest_expressed_genes	Highest Expressed Genes Plot.

Common

xyplot	Scatter Plot.
xyplots	Scatter Plots.

Heatmap

heatmap	Heatmap.
matrixplot	Matrix plot.
dotplot	Dotplot.
stacked_violin	Stacked Violin Plot.

Differential Expression

volcano	Volcano plot.
volcanos	Grid of volcano plots, one per group.

Dimensionality Reduction

dimensional	Dimensionality reduction plot.
umap	UMAP Dimensionality reduction plot.
pca	PCA Dimensionality reduction plot.
tsne	tSNE Dimensionality reduction plot.
expression	Dimensionality reduction plot of expression data.
dimensionals	Grid of dimensionality reduction plots.
umaps	Grid of dimensionality reduction plots.
pcas	Grid of dimensionality reduction plots.
tsnes	Grid of dimensionality reduction plots.
expressions	Grid of dimensionality reduction plots.

Distributions

boxplot	Boxplot.
violin	Violin Plot.
boxplots	Boxplots.
violins	Violin Plots.

Spatial

spatial	Spatial plot.
spatials	Grid of spatial plots.

Data Frames

build_frame

Build a DataFrame from an AnnData object.

Layers

cluster_outlines	Layer of geom_path that outlines the given clusters.
ondata_legend	Layer of geom_text that places per-group labels at the center of each cluster.
arrow_axis	Layer of arrows as the X and Y axis to the plot.
stream	Layer of streams of velocities on the embedding.
bracket	Layer of geom_bracket annotating pairwise significance between groups.

Utility

show_colors	Show a grid of hand-picked colors.
get_mapping	Returns the mapping of the plot as a dict.
retrieve	Retrieves the dataframe from a PlotSpec or SupPlotsSpec using the index.
slice	Slice a grid object (SupPlotsSpec) with the given index.
save	Convenience function for exporting plots.

Versions Information

versions

Print the in-use versions of the packages and python.