plot_pseudobeta.list {Coxmos}

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,
  show_percentage = TRUE,
  size_percentage = 3,
  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).

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).

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(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)