plot_r2: Plot (adjusted) r-squared for multiple models

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Plot (adjusted) r-squared for multiple models

Description

Plots regression model r-squared vs. model size (number of variables).

Usage

plot_r2(
  pve_list,
  model_names = NULL,
  line_color = "gray50",
  line_alpha = 0.5,
  line_type = "dashed",
  line_size = 1.5,
  point_color = NULL,
  palette = "Paired",
  point_alpha = 1,
  point_shape = 16,
  point_size = 5,
  label_size = 5,
  label_line_size = 0.75,
  label_line_alpha = 0.5,
  title = NULL,
  x_title = "Model complexity (no. of variables)",
  y_title = "Variance explained",
  legend_title = NULL,
  legend_position = "right",
  xlim_multiplier = 0.25,
  ylim_multiplier = 0.25
)

Arguments

pve_list	A list of lists containing regression model information. Each list must have the same element ordering, and the following elements and corresponding names are required: r2: The coefficient of determination. Can be calculated using get_matrix_r2(). Value can be NA if adjusted_r2 is numeric. adjusted_r2: The adjusted r2. Can be calculated using get_matrix_r2(). Value can be NA if r2 is numeric. num_model_vars: The number of variables in the model used to calculate r2 and adjusted_r2.
model_names	A vector of model names that follows the same ordering as the lists in pve_list. If not provided, a sequential numbering will be used.
line_color	A string for the line color between points.
line_alpha	A numeric for the line alpha value.
line_type	A string for the line type between points.
line_size	A numeric for the line size between points.
point_color	A vector of colors corresponding to the groups of points (r2 vs adjusted r2). If not specified, default colors from a color palette will be used.
palette	A string corresponding to a color palette from which point colors are chosen.
point_alpha	A numeric for the point alpha value.
point_shape	A numeric for the point shape.
point_size	A numeric for the point size.
label_size	A numeric for the label text size..
label_line_size	A numeric for the line thickness of the guide line from the label text to its corresponding point.
title	Plot title.
x_title	X-axis title.
y_title	Y-axis title.
legend_title	Legend title.
xlim_multiplier	A numeric constant used to increase or decrease the x-axis range.
ylim_multiplier	A numeric constant used to icnrease or decrease the y-axis range.
label_line_alpha.	A numeric for the line alpha value of the guide line from the label text to its corresponding point.

Details

Creates a scatterplot showing the tradeoff between variance explained of the outcome (e.g., gene expression) and model complexity. This function is designed to be a visualization helper function for the output from get_matrix_r2. It allows for the plotting of only r2, only adjusted r2, or both.

Value

A ggplot object.

See Also

get_matrix_r2 get_residual_matrix get_design_mat

bryancquach/omixjutsu documentation built on Jan. 29, 2023, 3:47 p.m.