API Reference

API pages include interactive (HTML) plots that would possibly not render correctly on a mobile device.

Cellestial is built on ggrust. Its layers, scales, themes and utilities follow the lets-plot API, so that reference covers further customization.

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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.

Heatmap

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

Distributions

boxplot	Boxplot.
violin	Violin Plot.
boxplots	Boxplots.
violins	Violin Plots.
histogram	Histogram.
histograms	Histograms.

Basic

plot	Base plot (for plots without data wrangling).
bar	Bar Plot.
scatter	Scatter Plot.

QC

markers	Grid of ranked genes per group.
ridge	Ridge Plot.
ridges	Ridge Plot.
elbow	Elbow Plot.
highest_expressed_genes	Highest Expressed Genes Plot.

Common

xyplot	Scatter Plot.
xyplots	Scatter Plots.

Differential Expression

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

Spatial

spatial	Spatial plot.
spatials	Grid of spatial plots.

Layers

cluster_outlines	Layer of geom_path that outlines the given clusters.
ondata_legend	Layer of geom_text that places per-group labels at median coordinates.
arrow_axis	Theme with arrows as the X and Y axis of the plot.
stream	Layer of streams of velocities on the embedding.
bracket	Layer of stat_compare_means annotating pairwise significance between groups.
borders	Add colored rectangles around panel, legend, and plot areas.

Data Frames

build_frame

Build a DataFrame from a single-cell object.

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.
get_figure	Get a single figure from a grid (SupPlotsSpec) by index.
get_figures	Get multiple figures from a grid (SupPlotsSpec) as a new grid.
save	Convenience function for exporting plots.
marker_genes	Select the top-ranked marker gene names from a precomputed ranking.
marker_genes_dict	Select the top-ranked marker gene names per group from a precomputed ranking.
layout	Arrange plots into a grid of rows, where each inner list is one row.

Colors

Color constants, shown by cl.show_colors().

cellestial.BLUE = "#377EB8"

cellestial.CHERRY = "#AF1740"

cellestial.LIGHT_GRAY = "#E6E6E6"

cellestial.ORANGE = "#F14A00"

cellestial.PINK = "#E73879"

cellestial.PURPLE = "#640D5F"

cellestial.RED = "#D2042D"

cellestial.SNOW = "#F9F9F9"

cellestial.TEAL = "#219B9D"

Datasets

pbmc3k	Download and load the preprocessed pbmc3k dataset.
pbmc_cite	Download and load a small multimodal CITE-seq PBMC dataset.
human_lymph_node	Download and load the preprocessed V1 Human Lymph Node Visium spatial dataset.
pancreas	Download and load the preprocessed endocrinogenesis day-15 pancreas dataset.
breast_cancer_atlas	Download and load the breast cancer cell atlas from CELLxGENE.
from_url	Download and load a dataset from a direct HTTP(S) URL.
from_cellxgene	Download and load a dataset from CELLxGENE by URL or UUID.

Versions Information

versions

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

cellestial.__version__

The installed cellestial version.