API Reference#

Declarative API Cheat Sheet#

Operator	Description	Example
`add_layer()`	Add a plotter to main canvas.	wb.add_layer(ColorMesh(data))
`add_left()`	Add to the left-side of main canvas.	wb.add_left(Numbers(data), size=1, pad=.1, name='left-plot')
`add_right()`	Add a plotter to the right-side of main canvas.	wb.add_right(Numbers(data))
`add_top()`	Add a plotter to the top-side of main canvas.	wb.add_top(Numbers(data))
`add_bottom()`	Add a plotter to the bottom-side of main canvas.	wb.add_bottom(Numbers(data))
`add_title()`	Add titles to the plot.	wb.add_title(top='Top Title', bottom='Bottom Title' left='Left Title', right='Right Title')
`add_dendrogram()`	Add a dendrogram to the plot, only available to ClusterBoard.	cb.add_dendrogram("left", data)
`group_cols()`	Split the main canvas horizontally, only available to ClusterBoard.	cb.group_cols(labels=[1, 1, 2, 2], order=[2, 1])
`group_rows()`	Split the main canvas vertically, only available to ClusterBoard.	cb.group_rows(labels=[1, 1, 2, 2], order=[2, 1])
`cut_cols()`	Split the main canvas horizontally, only available to ClusterBoard.	cb.cut_cols([5])
`cut_rows()`	Split the main canvas vertically, only available to ClusterBoard.	cb.cut_rows([5])
`add_legends()`	Add legends to the plots.	wb.add_legends()
`add_canvas()`	Add a plotter to a chosen side of main plot.	wb.add_canvas("right", Numbers(data))
`add_pad()`	Add white space between plot.	wb.add_pad("right", 1)
`set_margin()`	Add white space surrounding the figure.	wb.set_margin(1)
`render()`	Render the plot.	wb.render()
`save()`	Save the plot to a file.	wb.save("output.png", dpi=300)
`+`	Two canvas side by side, number will be added as white space	(wb1 + 1 + wb2).render()
`/`	Two canvas top and bottom, number will be added as white space	(wb1 / 1 / wb2).render()

High-Level Visualizations#

Heatmap Variants#

`Heatmap`	See `ColorMesh` for details
`SizedHeatmap`	Sized Heatmap
`CatHeatmap`	Categorical Heatmap

Layers Heatmap#

`Layers`
`LayersMesh`	The mesh that draw customized elements in multi-layers

UpSet plots#

`Upset`	Upset Plot
`UpsetData`	Handle multiple sets

OncoPrint#

Plotters#

Mesh#

`ColorMesh`	Continuous Heatmap
`Colors`	Categorical colors/heatmap
`SizedMesh`	Mesh for sized elements
`MarkerMesh`	The mesh that draw marker shape
`TextMesh`	The mesh that draw text on each cell

Seaborn plots#

`Bar`	Wrapper for seaborn's barplot
`Box`	Wrapper for seaborn's boxplot
`Boxen`	Wrapper for seaborn's boxenplot
`Violin`	Wrapper for seaborn's violinplot
`Point`	Wrapper for seaborn's pointplot
`Strip`	Wrapper for seaborn's stripplot
`Swarm`	Wrapper for seaborn's swarmplot

Other plots#

`Area`	Area plot
`Arc`	Arc diagram.
`Numbers`	Show numbers in bar plot
`StackBar`	Stacked Bar
`CenterBar`	Two comparable bar plots with center line
`SeqLogo`	Sequence logo

Text Label#

`Labels`	Add text labels
`AnnoLabels`	Annotate a few rows or columns
`Title`	Add a title
`Chunk`	Mark groups
`FixedChunk`	Mark groups with fixed order

Main Canvas#

`WhiteBoard`	The base class that handle all rendering process
`ClusterBoard`	A main canvas class that can handle cluster data
`LegendMaker`	The factory class to handle legends
`ZeroWidth`	A utility class to initialize a canvas with zero width
`ZeroHeight`	A utility class to initialize a canvas with zero height
`ZeroWidthCluster`	A utility class to initialize a canvas with zero width and cluster data
`ZeroHeightCluster`	A utility class to initialize a canvas with zero height and cluster data

Layout Engine#

`CrossLayout`	The X-layout engine
`CompositeCrossLayout`	A class to layout multiple Cross Layouts

Data Manipulation#

A helper class to handle data

Render plan#

`RenderPlan`	The base class for every plotter in Marsilea
`RenderSpec`	The container class that holds the rendering data and parameters for each axes