plotly: Initiate a plotly visualization
In tidyseurat: Brings Seurat to the Tidyverse

plotly

R Documentation

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

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"
)

## S3 method for class 'tbl_df'
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"
)

## S3 method for class 'Seurat'
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))