plot_observation.pseudobeta.list function

plot_observation.pseudobeta.list

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

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).

Returns

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.

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])

Author(s)

Pedro Salguero Garcia. Maintainer: pedsalga@upv.edu.es