plot_pseudobeta.list: plot_pseudobeta.list

In Coxmos: Cox MultiBlock Survival

plot_pseudobeta.list

Description

Run the function "plot_pseudobeta" for a list of models. More information in "?plot_pseudobeta".

Usage

plot_pseudobeta.list(
  lst_models,
  error.bar = TRUE,
  onlySig = FALSE,
  alpha = 0.05,
  zero.rm = TRUE,
  top = NULL,
  auto.limits = TRUE,
  selected_variables = NULL,
  show_percentage = TRUE,
  size_percentage = 3,
  title = NULL,
  title_size_text = 15,
  subtitle = NULL,
  subtitle_size_text = 12,
  legend.position = "right",
  legend_title = "Method",
  legend_size_text = 12,
  x_axis_size_text = 10,
  y_axis_size_text = 10,
  label_x_axis_size = 10,
  label_y_axis_size = 10,
  verbose = FALSE
)

Arguments

lst_models	List of Coxmos models.
error.bar	Logical. Show error bar (default: TRUE).
onlySig	Logical. Compute pseudobetas using only significant components (default: FALSE).
alpha	Numeric. Numerical values are regarded as significant if they fall below the threshold (default: 0.05).
zero.rm	Logical. Remove variables with a pseudobeta equal to 0 (default: TRUE).
top	Numeric. Show "top" first variables with the higher pseudobetas in absolute value. If top = NULL, all variables are shown (default: NULL).
auto.limits	Logical. If "auto.limits" = TRUE, limits are detected automatically (default: TRUE).
selected_variables	Character. Name of survival model variables to performed a custom selection (default: NULL).
show_percentage	Logical. If show_percentage = TRUE, it shows the contribution percentage for each variable to the full model (default: TRUE).
size_percentage	Numeric. Size of percentage text (default: 3).
title	Character. Plot title (default: NULL).
title_size_text	Numeric. Text size for title (default: 15).
subtitle	Character. Plot subtitle (default: NULL).
subtitle_size_text	Numeric. Text size for subtitle (default: 12).
legend.position	Character. Legend position. Must be one of the following: "top", "bottom", "right" or "left (default: "right").
legend_title	Character. Legend title (default: "Method").
legend_size_text	Numeric. Text size for legend title (default: 12).
x_axis_size_text	Numeric. Text size for x axis (default: 10).
y_axis_size_text	Numeric. Text size for y axis (default: 10).
label_x_axis_size	Numeric. Text size for x label axis (default: 10).
label_y_axis_size	Numeric. Text size for y label axis (default: 10).
verbose	Logical. If verbose = TRUE, extra messages could be displayed (default: FALSE).

Value

A list containing the following elements per model: plot: Depending on the model type, this can either be a single ggplot object visualizing the pseudo-beta coefficients for the original variables in a single block PLS-Cox model, or a list of ggplot objects for each block in a multiblock PLS-Cox model. Each plot provides a comprehensive visualization of the pseudo-beta coefficients, potentially including error bars, significance filtering, and variable contribution percentages. beta: A matrix or list of matrices (for multiblock models) containing the computed pseudo-beta coefficients for the original variables. These coefficients represent the influence of each original variable on the survival prediction. sd.min: A matrix or list of matrices (for multiblock models) representing the lower bounds of the error bars for the pseudo-beta coefficients. sd.max: A matrix or list of matrices (for multiblock models) representing the upper bounds of the error bars for the pseudo-beta coefficients.

Author(s)

Pedro Salguero Garcia. Maintainer: [e-mail]

Examples

data("X_proteomic")
data("Y_proteomic")
X <- X_proteomic[,1:50]
Y <- Y_proteomic
splsicox.model <- splsicox(X, Y, n.comp = 2, penalty = 0.5, x.center = TRUE, x.scale = TRUE)
splsdrcox.model <- splsdrcox_penalty(X, Y, n.comp = 2, penalty = 0.5,
x.center = TRUE, x.scale = TRUE)
lst_models = list("sPLSICOX" = splsicox.model, "sPLSDRCOX" = splsdrcox.model)
plot_pseudobeta.list(lst_models = lst_models)

Coxmos documentation built on April 4, 2025, 12:20 a.m.