plotComb {dtComb}

Plot the combination scores using the training model

Description

The plotComb a function that generates plots from the training model. The function takes argument model. The outputs of the function are three different plots generated from the combination scores.

Usage

plotComb(model, status)

Arguments

model

a list object where the parameters from the training model are saved.

status

a factor vector that includes the actual disease status of the patients

Value

A data.frame plots

Author(s)

Serra Ilayda Yerlitas, Serra Bersan Gengec, Necla Kochan, Gozde Erturk Zararsiz, Selcuk Korkmaz, Gokmen Zararsiz

Examples

# call data
data(exampleData1)

# define the function parameters
markers <- exampleData1[, -1]
status <- factor(exampleData1$group, levels = c("not_needed", "needed"))
event <- "needed"

score1 <- linComb(
  markers = markers, status = status, event = event,
  method = "scoring", resample = "none",
  standardize = "none", direction = "<", cutoff.method = "Youden"
)

plotComb(score1, status)

score2 <- nonlinComb(
  markers = markers, status = status, event = event,
  method = "nsgam", resample = "cv", include.interact = FALSE, direction = "<",
  standardize = "zScore", cutoff.method = "Youden"
)

plot.score2 <- plotComb(score2, status)

score3 <- mathComb(
  markers = markers, status = status, event = event,
  method = "distance", distance = "euclidean", direction = "auto",
  standardize = "tScore", cutoff.method = "Youden"
)

plot.score3 <- plotComb(score3, status)