plot_ci function

Plot the confidence interval for correlation

This function plots the 95% confidence interval for Pearson's correlation coefficient generated by the function corr_ci.

plot_ci(
  object,
  fill = NULL,
  position.fill = 0.3,
  x.lab = NULL,
  y.lab = NULL,
  y.lim = NULL,
  y.breaks = waiver(),
  shape = 21,
  col.shape = "black",
  fill.shape = "orange",
  size.shape = 2.5,
  width.errbar = 0.2,
  main = TRUE,
  invert.axis = TRUE,
  reorder = TRUE,
  legend.position = "bottom",
  plot_theme = theme_metan()
)

Arguments

• object: An object generate by the function corr_ci()
• fill: If corr_ci() is computed with the argument by use fill to fill the shape by each level of the grouping variable by.
• position.fill: The position of shapes and errorbar when fill is used. Defaults to 0.3.
• x.lab: The label of x-axis, set to 'Pairwise combinations'. New arguments can be inserted as x.lab = 'my label'.
• y.lab: The label of y-axis, set to 'Pearson's correlation coefficient' New arguments can be inserted as y.lab = 'my label'.
• y.lim: The range of x-axis. Default is NULL. The same arguments than x.lim can be used.
• y.breaks: The breaks to be plotted in the x-axis. Default is authomatic breaks. The same arguments than x.breaks can be used.
• shape: The shape point to represent the correlation coefficient. Default is 21 (circle). Values must be between 21-25: 21 (circle), 22 (square), 23 (diamond), 24 (up triangle), and 25 (low triangle).
• col.shape: The color for the shape edge. Set to black.
• fill.shape: The color to fill the shape. Set to orange.
• size.shape: The size for the shape point. Set to 2.5.
• width.errbar: The width for the errorbar showing the CI.
• main: The title of the plot. Set to main = FALSE to ommite the plot title.
• invert.axis: Should the names of the pairwise correlation appear in the y-axis?
• reorder: Logical argument. If TRUE (default) the pairwise combinations are reordered according to the correlation coefficient.
• legend.position: The position of the legend when using fill argument. Defaults to "bottom".
• plot_theme: The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details, see ggplot2::theme().

Returns

An object of class gg, ggplot.

Examples

library(metan)
library(dplyr)
# Traits that contains "E"
data_ge2 %>%
  select(contains('E')) %>%
  corr_ci() %>%
  plot_ci()

# Group by environment
# Traits PH, EH, EP, EL, and ED
# Select only correlations with PH

data_ge2 %>%
 corr_ci(PH, EP, EL, ED, CW,
         sel.var = "PH",
         by = ENV) %>%
 plot_ci(fill = ENV)