scatter_data_frame: Scatterplot Function for Data Frame
In bergsmat/metaplot: Data-Driven Plot Design

scatter_data_frame

R Documentation

Scatterplot Function for Data Frame

Description

Scatterplot function for class 'data.frame'.

Usage

scatter_data_frame(
  x,
  yvar,
  xvar,
  groups = NULL,
  facets = NULL,
  log = metOption("log_scatter", FALSE),
  ylog = metOption("ylog_scatter", log),
  xlog = metOption("xlog_scatter", log),
  crit = metOption("crit_scatter", 1.3),
  yref = metOption("yref_scatter", "metaplot_ref"),
  xref = metOption("xref_scatter", "metaplot_ref"),
  ylab = metOption("ylab_scatter", "axislabel"),
  xlab = metOption("xlab_scatter", "axislabel"),
  ysmooth = metOption("ysmooth_scatter", FALSE),
  xsmooth = metOption("xsmooth_scatter", FALSE),
  iso = metOption("iso_scatter", FALSE),
  na.rm = metOption("na.rm_scatter", TRUE),
  aspect = metOption("aspect_scatter", 1),
  space = metOption("space_scatter", "right"),
  key = metOption("key_scatter", "metaplot_key"),
  as.table = metOption("as.table_scatter", TRUE),
  prepanel = metOption("prepanel_scatter", NULL),
  isoprepanel = metOption("isoprepanel_scatter", "iso_prepanel"),
  scales = metOption("scales_scatter", NULL),
  panel = metOption("panel_scatter", "scatter_panel"),
  points = metOption("points_scatter", TRUE),
  colors = metOption("colors_scatter", NULL),
  fill = metOption("fill_scatter", NULL),
  symbols = metOption("symbols_scatter", NULL),
  sizes = metOption("sizes_scatter", 1),
  types = metOption("types_scatter", "solid"),
  widths = metOption("widths_scatter", 1),
  lines = metOption("lines_scatter", FALSE),
  main = metOption("main_scatter", NULL),
  sub = metOption("sub_scatter", NULL),
  subscripts = metOption("subscripts_scatter", TRUE),
  settings = metOption("settings_scatter", NULL),
  padding = metOption("padding_scatter", 1),
  ref.col = metOption("ref.col_scatter", "grey"),
  ref.lty = metOption("ref.lty_scatter", "solid"),
  ref.lwd = metOption("ref.lwd_scatter", 1),
  ref.alpha = metOption("ref.alpha_scatter", 1),
  xref.col = metOption("xref.col_scatter", NULL),
  xref.lty = metOption("xref.lty_scatter", NULL),
  xref.lwd = metOption("xref.lwd_scatter", NULL),
  xref.alpha = metOption("xref.alpha_scatter", NULL),
  yref.col = metOption("yref.col_scatter", NULL),
  yref.lty = metOption("yref.lty_scatter", NULL),
  yref.lwd = metOption("yref.lwd_scatter", NULL),
  yref.alpha = metOption("yref.alpha_scatter", NULL),
  smooth.lty = metOption("smooth.lty_scatter", "dashed"),
  smooth.lwd = metOption("smooth.lwd_scatter", 1),
  smooth.alpha = metOption("smooth.alpha_scatter", 1),
  fit = metOption("fit_scatter", conf),
  fit.lty = metOption("fit.lty_scatter", "solid"),
  fit.lwd = metOption("fit.lwd_scatter", 1),
  fit.alpha = metOption("fit.alpha_scatter", 1),
  conf = metOption("conf_scatter", FALSE),
  conf.alpha = metOption("conf.alpha_scatter", 0.3),
  loc = metOption("loc_scatter", 0),
  global = metOption("global_scatter", FALSE),
  global.col = metOption("global.col_scatter", "grey"),
  global.fill = metOption("global.fill_scatter", "grey"),
  msg = metOption("msg_scatter", "metastats"),
  gg = metOption("gg_scatter", FALSE),
  verbose = metOption("verbose", FALSE),
  ...
)

Arguments

`x`	data.frame
`yvar`	character: y variable(s)
`xvar`	character: x variable
`groups`	optional grouping variable; ignored if more than one `yvar`
`facets`	optional conditioning variables
`log`	a default shared by `ylog` and `xlog`
`ylog`	log transform y axis (auto-selected if NA)
`xlog`	log transform x axis (auto-selected if NA)
`crit`	if ylog or xlog missing, log transform if mean/median ratio for non-missing values is greater than crit
`yref`	reference line from y axis; can be function(x = x, var = yvar, ...) or NULL to suppress
`xref`	reference line from x axis; can be function(x = x, var = xvar, ...) or NULL to suppress
`ylab`	y axis label; can be function(x = x, var = yvar, log = ylog, ..)
`xlab`	x axis label; can be function(x = x, var = xvar, log = xlog, ..)
`ysmooth`	supply loess smooth of y on x
`xsmooth`	supply loess smmoth of x on y
`iso`	logical: plot line of unity (auto-selected if NA); can be a (partial) list of aesthetics (col, lty, lwd, alpha)
`na.rm`	whether to remove data points with one or more missing coordinates
`aspect`	passed to `bwplot` or ggplot; use 'fill', NA, or NULL to calculate automatically
`space`	location of key (right, left, top, bottom)
`key`	list: passed to `xyplot` as `auto.key` or to `theme`; can be a function groups name, groups levels, points, lines, space, gg, and ... . See `metaplot_key`.
`as.table`	passed to `xyplot`
`prepanel`	passed to `xyplot` (guessed if NULL)
`isoprepanel`	passed to `xyplot` if iso is TRUE
`scales`	passed to `xyplot` or `facet_grid` or `facet_wrap` (guessed if NULL)
`panel`	name or definition of panel function
`points`	whether to plot points and fill for each group: logical, or alpha values between 0 and 1
`colors`	replacements for default colors in group order; can be length one integer to auto-select that many colors
`fill`	replacements for default fill colors in group order (means something different for `densplot_data_frame` and `categorical_data_frame`). Used for confidence regions and for filling symbols (pch 21:25).
`symbols`	replacements for default symbols in group order (i.e. values of pch)
`sizes`	replacements for default symbol sizes in group order
`types`	replacements for default line types in group order
`widths`	replacements for default line widths in group order
`lines`	whether to plot lines for each group: logical, or alpha values between 0 and 1. Points are connected in the order in which they appear in the data.
`main`	character, or a function of x, yvar, xvar, groups, facets, and log
`sub`	character, or a function of x, yvar, xvar, groups, facets, and log
`subscripts`	passed to `xyplot`
`settings`	default parameter settings: a list from which matching elements are passed to lattice (as par.settings) or to ggplot theme() and facet_wrap() or facet_grid(). `ncol` and `nrow` are used as layout indices for lattice (for homology with facet_wrap). Also merged with ....
`padding`	numeric (will be recycled to length 4) giving plot margins in default units: top, right, bottom, left (in multiples of 5.5 points for ggplot)
`ref.col`	default shared by `xref.col` and `yref.col`; can be length one integer to auto-select that many colors
`ref.lty`	default shared by `xref.lty` and `yref.lty`
`ref.lwd`	default shared by `xref.lwd` and `yref.lwd`
`ref.alpha`	default shared by `xref.alpha` and `yref.alpha`
`xref.col`	x reference line color (recycled)
`xref.lty`	x reference line type (recycled)
`xref.lwd`	x reference line size (recycled)
`xref.alpha`	x reference line alpha (recycled)
`yref.col`	y reference line color (recycled)
`yref.lty`	y reference line type (recycled)
`yref.lwd`	y reference line size (recycled)
`yref.alpha`	y reference line alpha (recycled)
`smooth.lty`	smooth line type
`smooth.lwd`	smooth line size
`smooth.alpha`	smooth alpha
`fit`	draw a linear fit of y ~ x
`fit.lty`	fit line type
`fit.lwd`	fit line size
`fit.alpha`	fit alpha
`conf`	logical, or width for a confidence region around a linear fit; passed to `region`; `TRUE` defaults to 95 percent confidence interval; may not make sense if xlog is TRUE
`conf.alpha`	alpha transparency for confidence region
`loc`	where to print statistics on a panel; suppressed for grouped plots an facetted ggplots
`global`	if TRUE, xsmooth, ysmooth, fit, and conf are applied to all data rather than groupwise
`global.col`	color for global aesthetics
`global.fill`	fill color for global aesthetics
`msg`	a function to print text on a panel: called with x values, y values, and ....
`gg`	logical: whether to generate `ggplot` instead of `trellis`
`verbose`	generate messages describing process
`...`	passed to called functions e.g., `region`

Examples

library(magrittr)
library(dplyr)
attr(Theoph$conc,'label') <- 'theophylline concentration'
attr(Theoph$conc,'guide') <- 'mg/L'
attr(Theoph$Time,'label') <- 'time'
attr(Theoph$Time,'guide') <- 'h'
attr(Theoph$Subject,'guide') <- '////'
scatter_data_frame(Theoph, 'conc', 'Time')
scatter_data_frame(Theoph, 'conc','Time', 'Subject')
scatter_data_frame(Theoph, 'conc','Time', facets = 'Subject')
scatter_data_frame(Theoph %>% filter(conc > 0), 'conc','Time', 'Subject',ylog = TRUE, yref = 5)
scatter_data_frame(Theoph, 'conc','Time', 'Subject',ylog = TRUE, yref = 5)
scatter_data_frame(Theoph, 'conc','Time', 'Subject',ysmooth = TRUE)
scatter_data_frame(Theoph, 'conc','Time', 'Subject',ysmooth = TRUE,global = TRUE)
scatter_data_frame(Theoph, 'conc','Time', conf = TRUE, loc = 3, yref = 6)
scatter_data_frame(Theoph, 'conc','Time', conf = TRUE, loc = 3, yref = 6)

bergsmat/metaplot documentation built on Feb. 21, 2024, 1:18 p.m.