plot_abs: Plotting Absolute Data Of Normalized Rootdetection Data Set

In PhilippJanitza/rootdetectR: Statistical analysis of rootdetection output with R

Plotting Absolute Data Of Normalized Rootdetection Data Set

Description

Absolute data are plotted as box plot, box and jitter plot combination or violin plot. Signifcances can be illustrated by letter encoding. There are a lot of possibilities to adjust the visualization.

Usage

plot_abs(
  root_norm,
  label_delim = ";",
  type = "jitter",
  size_jitter_dot = 2,
  plot_n = T,
  plot_colours,
  plot_title,
  size_plot_title = 14,
  y_label = "hypocotyl length [mm]",
  x_label = "",
  legend_label = "condition",
  size_legend_title = 12,
  size_legend_text = 10,
  width_lines = 0.5,
  width_axis = 0.5,
  size_x_axes = 9,
  size_y_axes = 9,
  size_n = 3,
  plot_significance = F,
  height_letter = 2,
  size_letter = 5,
  angle_letter = 0,
  plot_response = F,
  width_response = 0.4,
  alpha_response = 0.6
)

Arguments

root_norm	data.frame; normalized Rootdetection data set
label_delim	character; define how Factor1 and Factor2 are separated in Label
type	string; "box" = box plot, 'jitter' = box and jitter plot, 'violin' = violin plot
size_jitter_dot	number; defines the size of the dots in jitter plots
plot_n	logical; if TRUE sample size (n) will be plotted
plot_colours	vector; provide colors for the plot (same length than grouping variable)
plot_title	string; sets a plot title
size_plot_title	numeric; defines size of the plot title
y_label	string; axes description of y-axes
x_label	string; axes description of x-axes
legend_label	string; title of legend
size_legend_title	numeric; defines size of legend title
size_legend_text	numeric; defines size of legend text
width_lines	numeric; defines the line width of boxes or violins
width_axis	numeric; defines the line width of the axis
size_x_axes	numeric; defines size of x-axes labels
size_y_axes	numeric; defines size of y-axes labels
size_n	= numeric; defines size of n plotted (if plot_n = TRUE)
plot_significance	logical; if TRUE significance will be drawn as letters
height_letter	numeric; defines the position of the significance letters
size_letter	numeric; defines size of the significance letters
angle_letter	numeric, defines angle of significance letters
plot_response	logical; if TRUE response will be represented by a line between boxes
width_response	numeric; defines width of response lines
alpha_response	numeric; defines alpha level (visibility) of response lines

Value

plot; box, box jitter or violin plot of the absolute data

Examples

# plot without significance letters

root_norm <- norm_10mm_standard(root_output)
# box plot
plot_abs(root_norm, type = "box")
# box and jitter plot
plot_abs(root_norm, type = "jitter")
# violin plot
plot_abs(root_norm, type = "violin")
# provide own colours (standard r colours or hex-code)
# must have the same length than grouping variable 2 level(root_test_norm$Factor2)
plot_abs(root_norm, plot_colours = c("dodgerblue3", "firebrick2"))

# plot with significance letters

root_norm <- norm_10mm_standard(root_output)
plot_abs(root_norm, plot_significance = TRUE)

# all customizable plotting parameters have a default value
plot_abs(root_norm,
  label_delim = ";",
  type = "jitter", size_jitter_dot = 2,
  plot_n = TRUE,
  plot_colours = c("cornflowerblue", "coral2"),
  plot_title = "My Plot", size_plot_title = 14,
  y_label = "length mm", x_label = "",
  legend_label = "condition", size_legend_title = 12, size_legend_text = 10,
  width_lines = 0.5, width_axis = 0.5,
  size_x_axes = 9, size_y_axes = 9,
  size_n = 3,
  plot_significance = TRUE, height_letter = 5, size_letter = 5, angle_letter = 0,
  plot_response = TRUE, width_response = 0.4, alpha_response = 0.6
)

PhilippJanitza/rootdetectR documentation built on Feb. 24, 2024, 6:46 a.m.