Package {canvasXpressDashboards}

Turn a data frame into a CanvasXpress data object

Description

Dashboards bind their panels to data shaped as a CanvasXpress object: the numeric columns are the *measures* ('y', one row per column of the frame) and every other column is an *annotation* of the records ('x'). Rows are the records. This is the orientation the dashboard templates expect (more rows than numeric columns).

Usage

cxd_data(df, id = NULL)

Arguments

Value

A list with 'y' ('vars', 'smps', 'data') and, when there are annotation columns, 'x'. Missing values are kept as 'NA' and become JSON 'null'.

Examples

cxd_data(data.frame(id = c("a", "b"), age = c(40, 50), arm = c("Drug", "Placebo")), id = "id")

Read a dashboard spec

Description

Accepts what is convenient: a list, a JSON string, or the path of a '.json' file (for example one saved from the dashboards builder or returned by the 'suggest_canvasxpress_dashboard' MCP tool).

Usage

cxd_read_spec(spec)

Arguments

Value

The spec as a list.

Render a canvasxpress-dashboards dashboard

Description

Renders a multi-panel, linked dashboard described by one JSON spec - or builds a whole dashboard from a data frame. Works in R Markdown, Quarto, the RStudio viewer, 'htmlwidgets::saveWidget()' and Shiny (see [cxdashboardOutput()]).

Usage

cxdashboard(
  spec = NULL,
  data = NULL,
  id = NULL,
  title = NULL,
  theme = NULL,
  engine = c("cdn", "canvasXpress"),
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

Details

Give **either** a 'spec' (rendered as written) **or** 'data' (a dashboard is suggested for it).

With 'data', the dashboard is assembled in the browser from the same templates as the dashboards wizard: a patient cohort (a numeric time column such as 'os_months' or 'time' plus a numeric 0/1 event column) gets filters, a Kaplan-Meier curve, a measure by group and against time, and a case card; a per-sample sequencing run-QC table (three or more of reads, mapping, quality, duplication, GC, insert size, coverage, adapter, contamination) gets filters, depth per sample, mapping against duplication and quality by lane or batch. Clicking a patient or sample loads its record into the case card. If no template fits, the widget says so instead of guessing; pass a 'spec'.

Arrays in a hand-built 'spec' list must stay arrays: write 'xAxis = I("age")', not 'xAxis = "age"' (a length-one vector would be sent as a plain string). A spec read from JSON (a string or a file) needs no care.

The insights strip ('insights' in a spec) is computed by the dashboards server and is not shown by this widget.

Value

An 'htmlwidget'.

Examples

spec <- list(
  id = "demo", title = "Demo",
  layout = list(cols = 12, rowHeight = 30,
    items = list(list(panel = "bars", x = 0, y = 0, w = 12, h = 10))),
  data = list(d = list(kind = "inline", value = cxd_data(
    data.frame(region = c("N", "S", "E"), revenue = c(10, 20, 15)), id = NULL))),
  panels = list(bars = list(dataRef = "d", config = list(graphType = "Bar", xAxis = I("revenue"))))
)
if (interactive()) cxdashboard(spec)

Drive a rendered dashboard from the Shiny server

Description

Drive a rendered dashboard from the Shiny server

Usage

cxdashboardProxy(outputId, session = shiny::getDefaultReactiveDomain())

cxd_set_param(proxy, name, value)

cxd_focus_panel(proxy, panel)

Arguments

Value

'cxdashboardProxy()' a proxy object; the 'cxd_*' functions return it invisibly.

Examples

## Not run: 
observeEvent(input$load_p018, cxd_set_param(cxdashboardProxy("dash"), "case", "P018"))

## End(Not run)

Shiny bindings for cxdashboard

Description

Output and render functions, plus a proxy to drive a rendered dashboard from the server.

Usage

cxdashboardOutput(outputId, width = "100%", height = "auto")

renderCxdashboard(expr, env = parent.frame(), quoted = FALSE)

Arguments

Details

Besides the usual widget behaviour, a dashboard reports back to the app through two inputs named after its output id: ‘input$<id>_params' (a named list of the dashboard’s current parameters; it updates whenever a click action, control or [cxd_set_param()] changes one - for the case-card dashboards, 'input$<id>_params$case' is the patient or sample last clicked) and, for a dashboard suggested from 'data', 'input$<id>_template' ('"cohort"' or '"ngs-qc"').

Value

'cxdashboardOutput()' an output element; 'renderCxdashboard()' a render function.