Shiny for Python

geneviewer.shiny has the output of a chart, its renderer and zoom_to(). It needs the shiny extra:

pip install "geneviewer-py[shiny]"

A chart in an app

output_geneviewer() puts the chart in the page, and a function decorated with @render_geneviewer returns the chart to draw. When an input the function reads changes, the chart is drawn again in place:

from shiny import App, ui

from geneviewer import GC, datasets
from geneviewer.shiny import output_geneviewer, render_geneviewer

clusters = datasets.load("ophA_clusters")

app_ui = ui.page_fluid(
    ui.input_select("theme", "Theme", ["default", "dark", "vintage"]),
    output_geneviewer("chart", height="300px"),
)


def server(input, output, session):
    @render_geneviewer
    def chart():
        return (
            GC(clusters, cluster="cluster", group="class", height="300px")
            .labels("name")
            .theme(input.theme())
        )


app = App(app_ui, server)

Events

The events switched on with .events() set inputs named after the output: for the output "chart", a selected gene is input.chart_select().

Input	Value	Switched on by
input.<id>_click()	The element clicked	click=True (the default)
input.<id>_dblclick()	The element double-clicked	dblclick=True
input.<id>_select()	The element selected last	select=True
input.<id>_selection()	Every selected element, as a list	select=True
input.<id>_drag()	An element moved by dragging, and its offset	drag=True
input.<id>_moves()	The elements a reset, undo or redo moved	drag=True
input.<id>_zoom()	The window of the zoom slider	zoom=True
input.<id>_rendered()	The chart was drawn	rendered=True

Each value is a dict; Events describes what each holds. An input is set again when the same event happens twice, so a second click on the same gene reaches the server too.

from shiny import App, render, ui

from geneviewer import GC, datasets
from geneviewer.shiny import output_geneviewer, render_geneviewer

clusters = datasets.load("ophA_clusters")

app_ui = ui.page_fluid(
    output_geneviewer("chart", height="300px"),
    ui.output_text("selected"),
)


def server(input, output, session):
    @render_geneviewer
    def chart():
        return (
            GC(clusters, cluster="cluster", group="class", height="300px")
            .labels("name")
            .events(select=True)
        )

    @render.text
    def selected():
        gene = input.chart_select()
        return f"Selected: {gene['data']['name']}" if gene else "Click a gene"


app = App(app_ui, server)

Moving the zoom slider

zoom_to() sets the window of a chart with a zoom slider (.zoom()) from the server, without drawing the chart again:

from shiny import App, reactive, ui

from geneviewer import GC, datasets
from geneviewer.shiny import output_geneviewer, render_geneviewer, zoom_to

clusters = datasets.load("ophA_clusters")

app_ui = ui.page_fluid(
    ui.input_action_button("first_half", "Zoom to the first half"),
    ui.input_action_button("everything", "Show everything"),
    output_geneviewer("chart", height="300px"),
)


def server(input, output, session):
    @render_geneviewer
    def chart():
        return GC(clusters, cluster="cluster", group="class", height="300px").zoom()

    @reactive.effect
    @reactive.event(input.first_half)
    def _():
        zoom_to("chart", [0, 0.5])

    @reactive.effect
    @reactive.event(input.everything)
    def _():
        zoom_to("chart", None)


app = App(app_ui, server)

Toolbar icons

The toolbar's own icons need nothing. Custom icons, set with .toolbar(), are Font Awesome icons by name, such as "camera", and need Font Awesome on the page. A Shiny for Python page does not load it, so add it to the UI:

from shiny import ui

font_awesome = ui.head_content(
    ui.tags.link(
        rel="stylesheet",
        href="https://cdn.jsdelivr.net/npm/@fortawesome/fontawesome-free@6/css/all.min.css",
    )
)

An example app

The package's repository has an app with three charts, a panel that shows each event input, and buttons that move the zoom slider:

git clone https://github.com/nvelden/geneviewer-py
shiny run geneviewer-py/examples/shiny/app.py