plot_ly: Initiate a plotly visualization

In stemangiola/tidySCE: Brings SingleCellExperiment to the Tidyverse

Initiate a plotly visualization

Description

This function maps R objects to plotly.js, an (MIT licensed) web-based interactive charting library. It provides abstractions for doing common things (e.g. mapping data values to fill colors (via color) or creating animations (via frame)) and sets some different defaults to make the interface feel more 'R-like' (i.e., closer to plot() and ggplot2::qplot()).

Usage

## S3 method for class 'SingleCellExperiment'
plot_ly(
  data = data.frame(),
  ...,
  type = NULL,
  name = NULL,
  color = NULL,
  colors = NULL,
  alpha = NULL,
  stroke = NULL,
  strokes = NULL,
  alpha_stroke = 1,
  size = NULL,
  sizes = c(10, 100),
  span = NULL,
  spans = c(1, 20),
  symbol = NULL,
  symbols = NULL,
  linetype = NULL,
  linetypes = NULL,
  split = NULL,
  frame = NULL,
  width = NULL,
  height = NULL,
  source = "A"
)

Arguments

data	A data frame (optional) or crosstalk::SharedData object.
...	Arguments (i.e., attributes) passed along to the trace type. See schema() for a list of acceptable attributes for a given trace type (by going to traces -> type -> attributes). Note that attributes provided at this level may override other arguments (e.g. plot_ly(x = 1:10, y = 1:10, color = I("red"), marker = list(color = "blue"))).
type	A character string specifying the trace type (e.g. "scatter", "bar", "box", etc). If specified, it always creates a trace, otherwise
name	Values mapped to the trace's name attribute. Since a trace can only have one name, this argument acts very much like split in that it creates one trace for every unique value.
color	Values mapped to relevant 'fill-color' attribute(s) (e.g. fillcolor, marker.color, textfont.color, etc.). The mapping from data values to color codes may be controlled using colors and alpha, or avoided altogether via I() (e.g., color = I("red")). Any color understood by grDevices::col2rgb() may be used in this way.
colors	Either a colorbrewer2.org palette name (e.g. "YlOrRd" or "Blues"), or a vector of colors to interpolate in hexadecimal "#RRGGBB" format, or a color interpolation function like colorRamp().
alpha	A number between 0 and 1 specifying the alpha channel applied to color. Defaults to 0.5 when mapping to fillcolor and 1 otherwise.
stroke	Similar to color, but values are mapped to relevant 'stroke-color' attribute(s) (e.g., marker.line.color and line.color for filled polygons). If not specified, stroke inherits from color.
strokes	Similar to colors, but controls the stroke mapping.
alpha_stroke	Similar to alpha, but applied to stroke.
size	(Numeric) values mapped to relevant 'fill-size' attribute(s) (e.g., marker.size, textfont.size, and error_x.width). The mapping from data values to symbols may be controlled using sizes, or avoided altogether via I() (e.g., size = I(30)).
sizes	A numeric vector of length 2 used to scale size to pixels.
span	(Numeric) values mapped to relevant 'stroke-size' attribute(s) (e.g., marker.line.width, line.width for filled polygons, and error_x.thickness) The mapping from data values to symbols may be controlled using spans, or avoided altogether via I() (e.g., span = I(30)).
spans	A numeric vector of length 2 used to scale span to pixels.
symbol	(Discrete) values mapped to marker.symbol. The mapping from data values to symbols may be controlled using symbols, or avoided altogether via I() (e.g., symbol = I("pentagon")). Any pch value or symbol name may be used in this way.
symbols	A character vector of pch values or symbol names.
linetype	(Discrete) values mapped to line.dash. The mapping from data values to symbols may be controlled using linetypes, or avoided altogether via I() (e.g., linetype = I("dash")). Any lty (see par) value or dash name may be used in this way.
linetypes	A character vector of lty values or dash names
split	(Discrete) values used to create multiple traces (one trace per value).
frame	(Discrete) values used to create animation frames.
width	Width in pixels (optional, defaults to automatic sizing).
height	Height in pixels (optional, defaults to automatic sizing).
source	a character string of length 1. Match the value of this string with the source argument in event_data() to retrieve the event data corresponding to a specific plot (shiny apps can have multiple plots).

Details

Unless type is specified, this function just initiates a plotly object with 'global' attributes that are passed onto downstream uses of add_trace() (or similar). A formula must always be used when referencing column name(s) in data (e.g. plot_ly(mtcars, x = ~wt)). Formulas are optional when supplying values directly, but they do help inform default axis/scale titles (e.g., plot_ly(x = mtcars$wt) vs plot_ly(x = ~mtcars$wt))

Value

'plotly'

Author(s)

Carson Sievert

References

https://plotly-r.com/overview.html

See Also

• For initializing a plotly-geo object: plot_geo()

• For initializing a plotly-mapbox object: plot_mapbox()

• For translating a ggplot2 object to a plotly object: ggplotly()

• For modifying any plotly object: layout(), add_trace(), style()

• For linked brushing: highlight()

• For arranging multiple plots: subplot(), crosstalk::bscols()

• For inspecting plotly objects: plotly_json()

• For quick, accurate, and searchable plotly.js reference: schema()

Examples

data(pbmc_small)
pbmc_small |> 
    plot_ly(x = ~ nCount_RNA, y = ~ nFeature_RNA)

stemangiola/tidySCE documentation built on Dec. 20, 2024, 10:19 p.m.