plot_observation.pseudobeta.list: plot_observation.pseudobeta.list

In Coxmos: Cox MultiBlock Survival

plot_observation.pseudobeta.list

Description

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

Usage

plot_observation.pseudobeta.list(
  lst_models,
  observation,
  error.bar = TRUE,
  onlySig = TRUE,
  alpha = 0.05,
  zero.rm = TRUE,
  txt.x.angle = 0,
  top = NULL,
  auto.limits = TRUE,
  show.betas = FALSE,
  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.
observation	Numeric matrix or data.frame. New explanatory variables (raw data) for one observation. Qualitative variables must be transform into binary variables.
error.bar	Logical. Show error bar (default: TRUE).
onlySig	Logical. Compute pseudobetas using only significant components (default: TRUE).
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).
txt.x.angle	Numeric. Angle of X text (default: 0).
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.betas	Logical. Show original betas (default: FALSE).
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 of lst_models length with a list of four elements per each model: plot: Linear prediction per variable. lp.var: Value of each linear prediction per variable. norm_observation: Observation normalized using the model information. observation: Observation used.

Author(s)

Pedro Salguero Garcia. Maintainer: [e-mail]

Examples

data("X_proteomic")
data("Y_proteomic")
set.seed(123)
index_train <- caret::createDataPartition(Y_proteomic$event, p = .5, list = FALSE, times = 1)
X_train <- X_proteomic[index_train,1:50]
Y_train <- Y_proteomic[index_train,]
X_test <- X_proteomic[-index_train,1:50]
Y_test <- Y_proteomic[-index_train,]
splsicox.model <- splsicox(X_train, Y_train, n.comp = 2, penalty = 0.5, x.center = TRUE,
x.scale = TRUE)
splsdrcox.model <- splsdrcox_penalty(X_train, Y_train, n.comp = 2, penalty = 0.5, x.center = TRUE,
x.scale = TRUE)
lst_models = list("sPLSICOX" = splsicox.model, "sPLSDRCOX" = splsdrcox.model)
plot_observation.pseudobeta.list(lst_models, observation = X_test[1,,drop=FALSE])

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