xMLparameters: Function to visualise cross-validation performance against...

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Description

xMLparameters is supposed to visualise cross-validation performance against tuning parameters.

Usage

xMLparameters(
data,
nD = c("auto", "1D", "2D", "3D"),
contour = TRUE,
main = "Repeated cross-validation",
xlab = NA,
ylab = NA,
zlab = NA,
clab = "AUC (repeated CV)",
nlevels = 50,
colormap = c("lightblue-lightyellow-darkorange-darkred", "bwr", "jet",
"gbr", "wyr",
"br", "yr", "rainbow", "wb"),
highlight = TRUE,
x.label.cex = 0.8,
x.label.srt = 30,
theta.3D = 40,
phi.3D = 25
)

Arguments

data	an object of the class "train" or "train.formula" (resulting from caret::train) used for 1D or 2D visualisation. Alternatively, it can be a data frame used for 2D or 3D visualisation
nD	an integer specifying the dimension of the visualisation. It can be one of '1D', '2D' and '3D' and 'auto' (if input data is a "train" object)
contour	logical to indicate whether coutour plot should be also included
main	a title for the plot
xlab	a title for the x axis
ylab	a title for the y axis
zlab	a title for the z axis
clab	a title for the colorbar
nlevels	the number of levels to partition the input matrix values. The same level has the same color mapped to
colormap	short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names
highlight	logical whether to highlight the point with the maximum value
x.label.cex	the x-axis label size
x.label.srt	the x-axis label angle (in degree from horizontal)
theta.3D	the azimuthal direction. By default, it is 40
phi.3D	the colatitude direction. By default, it is 20

Value

invisible

Note

none

See Also

xSparseMatrix

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
xMLparameters(df_fit, nD="2D")
xMLparameters(df_fit, nD="3D", theta.3D=40, phi.3D=60)

## End(Not run)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.