dash_bioOncoPrint Examples and Reference
see OncoPrint in action.
OncoPrint
An example of a default OncoPrint component without any extra properties.
library(jsonlite)
library(dash)
library(dashHtmlComponents)
library(dashCoreComponents)
library(dashBio)
app <- Dash$new()
data = read_json("https://git.io/oncoprint_dataset3.json")
app$layout(htmlDiv(list(
dashbioOncoPrint(
data = data,
id = "dashbio-default-oncoprint"
),
htmlDiv(id = 'default-oncoprint-output')
)))
app$callback(
output(id = "default-oncoprint-output", property = "children"),
params = list(
input(id = 'dashbio-default-oncoprint', property = "eventDatum")
),
update_output <- function(event_data) {
if (is.null(event_data)) {
return("There is no event data. Hover over or click on a part of the graph to generate event data.")
}
else {
return(htmlDiv(
sprintf("Event Data: %s", event_data)
))
}
}
)
app$run_server()
Customization
Colors
Change the color of specific mutations, as well as the background color.
library(dashBio)
data = read_json("https://git.io/oncoprint_dataset3.json")
dashbioOncoPrint(
data = data,
colorscale = list(
"MISSENSE" = "#e763fa",
"INFRAME" = "#E763FA"
),
backgroundcolor = "#F3F6FA"
)
Size And Spacing
Change the height and width of the component, and adjust the spacing between adjacent tracks.
library(dashBio)
data = read_json("https://git.io/oncoprint_dataset3.json")
dashbioOncoPrint(
data = data,
height = 800,
width = 500,
padding = 0.25
)
Legend And Overview
Show or hide the legend and/or overview heatmap.
library(dashBio)
data = read_json("https://git.io/oncoprint_dataset3.json")
dashbioOncoPrint(
data=data,
showlegend = FALSE,
showoverview = FALSE
)
OncoPrint Properties
Our recommended IDE for writing Dash apps is Dash Enterprise’s
Data Science Workspaces,
which has typeahead support for Dash Component Properties.
Find out if your company is using
Dash Enterprise.
id (character; optional):
The ID of this component, used to identify dash components in
callbacks. The ID needs to be unique to the component.
eventDatum (named list; optional):
A Dash prop that returns data on clicking, hovering or resizing the
viewer.
data (unnamed list; optional):
Input data, in CBioPortal format where each list entry is a dict
consisting of ‘sample’, ‘gene’, ‘alteration’, and ‘type’.
padding (numeric; default 0.05):
Adjusts the padding (as a proportion of whitespace) between two
tracks. Value is a ratio between 0 and 1. Defaults to 0.05 (i.e., 5
percent). If set to 0, plot will look like a heatmap.
colorscale (logical | named list; optional):
If not NULL, will override the default OncoPrint colorscale. Default
OncoPrint colorscale same as CBioPortal implementation. Make your own
colrscale as a {‘mutation’: COLOR} dict. Supported mutation keys are
[‘MISSENSE, ‘INFRAME’, ‘FUSION’, ‘AMP’, ‘GAIN’, ‘HETLOSS’, ‘HMODEL’,
‘UP’, ‘DOWN’] Note that this is NOT a standard plotly colorscale.
backgroundcolor (character; default 'rgb(190, 190, 190)'):
Default color for the tracks, in common name, hex, rgb or rgba format.
If left blank, will default to a light grey rgb(190, 190, 190).
range (unnamed list; default [NULL, NULL]):
Reset windowing to user preset on initial range or data change.
showlegend (logical; default TRUE):
Toogles whether or not to show a legend on the right side of the plot,
with mutation information.
showoverview (logical; default TRUE):
Toogles whether or not to show a heatmap overview of the tracks.
width (numeric | character; optional):
Width of the OncoPrint. Will disable auto-resizing of plots if set.
height (numeric | character; default 500):
Height of the OncoPrint. Will disable auto-resizing of plots if set.
loading_state (named list; optional):
Object that holds the loading state object coming from dash-renderer.
loading_state is a named list with keys:
-
component_name(character; optional):
Holds the name of the component that is loading. -
is_loading(logical; optional):
Determines if the component is loading or not. -
prop_name(character; optional):
Holds which property is loading.