plot_summary: Plot summary functions
In rolandrolandroland/rTEM: R package for statistical analysis of TEM data

plot_summary

R Documentation

Plot summary functions

Description

Plot the observed value with envelopes for expected values for summary function

Usage

plot_summary(
  func = "K",
  observed_values,
  envelopes,
  ...,
  pattern.colors = c(`Envelope 1` = "pink", `Envelope 2` = "gray", Observed = "blue"),
  fill.colors = NA,
  sqrt = "K",
  raw = "FALSE",
  base_value = "first",
  unit = "nm",
  K_cor = "trans",
  G_cor = "km",
  F_cor = "km",
  GXGH_cor = "km",
  GXHG_cor = "km",
  G2_cor = "km",
  alpha = 0.5,
  legend.key.size = 20,
  legend.text.size = 20,
  legend.position = c(0.75, 0.8),
  axis.title.size = 40,
  title = "",
  title.size = 40,
  axis.text.x.size = 40,
  axis.text.y.size = 40,
  linewidth = 0.5,
  env_linewidth = 0.5,
  linetype = "solid",
  env_linetype = "dashed"
)

Arguments

`func`	Summary function to plot.
`observed_values`	a list. observed summary function value. Must have one of the following structures Option 1: List of summary functionsobserved_values[[func]][[cor]] Option 2: List of lists of summary functionsobserved_values[[pattern_num]][[func]][[cor]] Option 2: Dataframeobserved_values[,c("r", y_value)]
`envelopes`	a list envelope values found by function such as `calc_summary_funcs`. Should be list of length equal to the number of envelopes. The structure should resemble: 'envelopes[[envelope_num]]$rrl_K[, c("r", "mmean")]'
`pattern.colors`	colors and names for envelope lines. MUST follow some formatting rules. Envelope names must come first. If each observed value corresponds to a different envelope, then the number of 'observed_values' must match 'length(envelopes)' and only the first '1:length(envelopes)' of 'pattern_colors' will be used. and must set 'base_value = "each"'. If not, each envelope and each observed value needs its own color. then the 'mmean' value from 'envelopes[[1]]' will be subtracted from each envelope and observed value.
`fill.colors`	colors and names for envelope fill. Match names to 'pattern.colors'. Recommended to leave as NA and it will automattically be set to match 'pattern.colors'
`sqrt`	either '"K", "all", or "none"'. If '"K"', then only `expression(tilde(K)[g](r))` will be found using the differences of the square roots, rather than differences. If '"all"', then all functions will be found using such. If '"none"' (or actually anything other than the first two options) then no square roots are taken. Ignored if 'raw = "TRUE"'
`base_value`	a character, either '"first" or "each"'. Does each observed value correspond to a different envelope? If yes, set to '"each"'. Otherwise, set to '"first"' and the envelopes[[1]] will be used for each
`unit`	a character. This will appear as the units in the x axis label
`K_cor`	edge correction(s) to be used when 'func = "K"'
`G_cor`	edge correction(s) to be used when 'func = "G"'
`F_cor`	edge correction(s) to be used when 'func = "F"'
`GXGH_cor`	edge correction(s) to be used when 'func = "GXGH"'
`GXHG_cor`	edge correction(s) to be used when 'func = "GXHG"'
`alpha`	numeric between 0 and 1. Transparency of envelopes
`legend.key.size`	numeric. size of legend key
`legend.text.size`	numeric. size of legend text
`axis.title.size`	numeric. Size of axis title
`title`	a character. Text for title
`title.size`	numeric. Title size
`axis.text.x.size`	numeric. size of text on x axis
`axis.text.y.size`	numeric. size of text on y axis
`linewidth`	numeric. Width of lines in plot
`env_linewidth`	numeric. Width of lines that make up envelope edges
`linetype`	a character. Type of lines that make up lines
`env_linetype`	a character. Type of lines that make up envelope lines
`raw.`	A logical. If TRUE, then no envelope mmeans are subtracted from each value
`legend.position.`	vector of 2 numerics. coordinates of legend