GC()

A gene cluster chart.

Build a chart from a data frame of genes, one row per gene, then add components with the methods. Each method returns a new chart. to_spec() gives the chart spec that the geneviewer JavaScript library draws.

Usage

from geneviewer import GC

GC(data, start, end, cluster, group, strand, width, height, style, save_button)

An argument shown without a default is optional too: left out, the chart keeps its default.

Arguments

Argument	Type	Description
data	pandas.DataFrame or str or path-like	The genes: one row per gene, with its start and end positions. Or a GenBank file, or a folder of them: their CDS are the genes, one cluster per file, with cluster and strand set to the columns of those names.
start	str	Column of start positions. Default "start".
end	str	Column of end positions. Default "end".
cluster	str, optional	Column of cluster names: one chart row per cluster.
group	str, optional	Column of groups, which set the gene colours and the legend.
strand	str, optional	Column of strands: 1, "forward", "sense" or "+" for the forward strand, and -1, 0, "reverse", "antisense", "complement" or "-" for the reverse strand. Default: from the order of start and end.
width	str or float	Width of the chart, e.g. "100%" or 500. Default "100%".
height	str or float	Height of the chart, e.g. "400px" or 300. Default "400px".
style	dict	CSS styles of the chart container, e.g. {"backgroundColor": "white"}.
save_button	bool	Whether the toolbar has the button to save the chart as SVG or PNG. Default True.

Examples

>>> import pandas as pd
>>> genes = pd.DataFrame({
...     "start": [10, 90, 130], "end": [40, 120, 160],
...     "name": ["a", "b", "c"], "group": ["A", "B", "A"],
... })
>>> chart = GC(genes, group="group", height="200px").labels("name")
>>> chart.to_spec()["labels"]
{'label': 'name'}