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Plot for each eigenSpline the automatically fitted spline, splines for all df and a spline at a chosen df

Source: R/df_search.R
get_eigen_DFoverlay_list.Rd

Plot for each eigenSpline the automatically fitted spline (red), splines for all possible df (grey) and a spline at a manually chosen df (blue).

Usage

get_eigen_DFoverlay_list(
  eigen,
  manualDf = 5,
  nPC = NA,
  step = NA,
  showPt = TRUE,
  autofit = TRUE
)

Arguments

eigen

A list of eigenSpline parameters as generated by get_eigen_spline, containing eigen$matrix, eigen$variance, eigen$model and eigen$countTP.

manualDf

(int) A manually selected df. Default is 5.

nPC

(int) The first n eigenSplines to plot. Default is NA, plot all eigenSplines.

step

(float) The df increment employed to plot splines over the range of df.

showPt

(bool) If True the eigenSpline data points are plotted. Default is TRUE.

autofit

(bool) If True the automatically fitted splines (using CV) are plotted. Default is TRUE.

Value

A list of ggplot2 plotObjects, one plot per eigenSpline. All results can be plotted using do.call(grid.arrange, returnedResult).

See also

Graphical implementation with santaR_start_GUI

Other DFsearch: get_eigen_DF(), get_eigen_spline(), get_param_evolution(), plot_nbTP_histogram(), plot_param_evolution()

Examples

## 8 subjects, 4 time-points, 3 variables
inputData  <- acuteInflammation$data[0:32,1:3]
ind        <- acuteInflammation$meta$ind[0:32]
time       <- acuteInflammation$meta$time[0:32]
eigen      <- get_eigen_spline(inputData, ind, time, nPC=NA, scaling="scaling_UV",
                               method="nipals", verbose=TRUE, centering=TRUE, ncores=0)
#> nipals calculated PCA
#> Importance of component(s):
#>                  PC1     PC2      PC3
#> R2            0.9272 0.06606 0.006756
#> Cumulative R2 0.9272 0.99324 1.000000
#> total time: 0.07 secs
paramSpace <- get_param_evolution(eigen, step=1)
plotList   <- get_eigen_DFoverlay_list(eigen,manualDf=3,step=0.5,showPt=TRUE,autofit=TRUE)
plotList[1]
#> [[1]]

#> 
# do.call(grid.arrange, plotList)