plot_p_vals: Plot p values functions
In rolandrolandroland/rTEM: R package for statistical analysis of TEM data

plot_p_vals

R Documentation

Plot p values functions

Description

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

Usage

plot_p_vals(
  func = "K",
  envelopes,
  pattern.colors = c(`Envelope 1` = "pink", `Envelope 2` = "gray", Observed = "blue"),
  envelope_names = c("r", "p"),
  base_value = "first",
  unit = "nm",
  K_cor = "trans",
  G_cor = "km",
  F_cor = "km",
  GXGH_cor = "km",
  GXHG_cor = "km",
  G2_cor = "km",
  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,
  linetype = "solid",
  env_linetype = "dashed"
)

Arguments

`func`	Summary function to plot.
`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.
`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"'
`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
`linetype`	a character. Type of lines that make up lines
`legend.position.`	vector of 2 numerics. coordinates of legend