API Reference#

Declarative API Cheat Sheet#

Operator	Showcase	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', bottom='Bottom' left='Left', right='Right')
`add_dendrogram()` Add a dendrogram to the plot, only available to ClusterBoard.		cb.add_dendrogram("right")
`group_cols()` Split the main canvas vertically by labeling columns, only available to ClusterBoard.		cb.group_cols(list("11223"))
`group_rows()` Split the main canvas horizontally by labeling rows, only available to ClusterBoard.		cb.group_rows(list("11223"))
`cut_cols()` Split the main canvas vertically by positions, only available to ClusterBoard.		cb.cut_cols([2, 4])
`cut_rows()` Split the main canvas horizontally by positions, only available to ClusterBoard.		cb.cut_rows([2, 4])
`add_legends()` Add legends to the plots.		wb.add_legends()
`add_canvas()` Add a empty canvas to a chosen side of main plot.		wb.add_canvas("right")
`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#

OncoPrint

OncoPrint plot

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
`Image`	Plot static images
`Emoji`	Have fun with emoji images
`Range`	Range plot

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 cross-layout engine
`CompositeCrossLayout`	A class to layout multiple Cross Layouts

Data Manipulation#

Deformation

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

Datasets#

load_data

To load marsilea dataset